Cancer diagnosis, treatment selection and treatment

ABSTRACT

The present invention provides assays, methods and systems for selecting an effective therapy for a subset of cancer patients having cancer cells with increased expression of BML and FANCI genes and/or having copy number increase in chromosome location 15q26 in the cancer cells and for treatment of such patients with the effective therapy of cancer patients based on the personalized cancer cell expression profile.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Divisional of U.S. patent Ser. No. 14/774,772,filed Sep. 11, 2015, which is a 35 U.S.C. § 371 National Phase EntryApplication of International Application No. PCT/US2014/025774, filedMar. 13, 2014, which designates the U.S., and which claims benefit under35 U.S.C. § 119(e) of U.S. Provisional Application No. 61/784,234, filedMar. 14, 2013, the contents of each of which are incorporated herein intheir entireties.

STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH

This invention was made with government support under Grant No. 2P50CA89393-06 awarded by the National Cancer Institute. The Government hascertain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Nov. 18, 2015, isnamed 701039-075882-US_SL.txt and is 512 bytes in size.

BACKGROUND

All publications herein are incorporated by reference to the same extentas if each individual publication or patent application was specificallyand individually indicated to be incorporated by reference. Thefollowing description includes information that may be useful inunderstanding the present invention. It is not an admission that any ofthe information provided herein is prior art or relevant to thepresently claimed invention, or that any publication specifically orimplicitly referenced is prior art.

Breast cancer is recognized as a collection of malignancies that allarise in the breast but are remarkably heterogeneous. Gene expressionarray experiments have defined at least 4 major subtypes: 1) Luminal A;2) Luminal B; 3) HER2+; and 4) Basal. There is a strong correlationbetween clinically defined triple negative breast cancer “TNBC”, asdefined by the absence of ER, PgR, and HER2 by standardimmunohistochemical staining, and the molecularly defined basal subtype.

TN breast cancer accounts for only 10-15% of all incident breast cancercases in the U.S., but results in a disproportionate number of breastcancer deaths. Women who are destined to develop metastatic TN diseasetypically experience a short disease free interval and have a higherdegree of lung and brain involvement than patients with luminal breastcancers. Furthermore, TN breast cancer is overrepresented among patientswho carry a deleterious BRCA1 germline alteration, and among women ofAfrican ancestry.

From a clinical perspective, despite substantial efforts to developnovel targeted agents, chemotherapy remains the mainstay of therapy forTN breast cancer, as trials evaluating a number of agents either in lieuof chemotherapy or in addition to chemotherapy have failed to produceany new agent that is capable of convincingly changing the naturalhistory of the disease. In the adjuvant setting, polychemotherapyregimens have been demonstrated to improve both disease-free survivaland overall survival. In the neoadjuvant setting, a favorable responseto chemotherapy is associated with a low chance of relapse at 5 years.In contrast, women who have a significant amount of residual diseaseafter a course of neoadjuvant chemotherapy have a particularly poorprognosis, with at least half experiencing a recurrence and death fromTN breast cancer within 5 years. In the metastatic setting, althoughpatients may respond to chemotherapy, the responses tend to be brief,and resistance tends to appear quickly.

Given the curative potential of chemotherapy in patients presenting withstage I-III TN breast cancer, and the initial responses (albeit oftenbrief) seen with chemotherapy in the metastatic setting, the generaldirection of targeted therapy development for TN breast cancer has beento combine targeted agents with chemotherapy. Thus, even with a growingnumber of targeted therapies under investigation for TN breast cancer,chemotherapy is likely to be a significant component of the treatment ofTN breast cancer for many years to come.

Across breast cancers as a whole, hormone receptor dependence and tumorproliferation appear to be associated with generic “chemosensitivity”.Using the 70 gene signature as an example, the current classifierstypically assign a “high-risk” status to the vast majority of TN tumors,and are also unable to define whether there may be differential benefitwith one class of chemotherapeutic agents over another. Thus, in bothclinical practice and in conventionally designed clinical trials, thetendency is to layer new therapies directly atop existing standards,increasing the risk of both overtreatment (because some, but not all ofthe administered therapies are efficacious) or undertreatment (becausethe tumor is not sensitive to any of the specific chemotherapeuticagents contained in the treatment regimen).

Accordingly, there exists a need in the art to identify the bestchemotherapy for each patient and to eliminate agents that are inert andresult in toxicity without benefit.

SUMMARY OF THE INVENTION

We provide novel methods, assays, systems and kits for determining if acancer patient is responsive to platinum-comprising therapy oranthracyclin therapy. These methods, assays, systems and kits provide asignificant improvement to the “trial-and-error”-therapies used incancer therapy. The methods allow one to personalize the treatment of acancer patient based on the cancer cells' specific protein/geneexpression profile. In other words, the methods apply the novel findingsof a cancer cells responses to cancer treatment methods and allowselection of the most likely effective therapy without delay and thussignificantly improve the patient's quality of life. Avoiding use ofineffective drugs will also provide a significant saving for the cost oftreatment for the cancer patient, as well avoiding exposure to sideeffects of ineffective drugs.

The invention is based, at least in part, on the discovery that patientshaving increased expression of BLM and/or FANCI genes compared to ahousekeeping gene or wild-type BRCA1 gene in their cancer cells arelikely to respond to platinum-comprising or anthracyclin-comprisingcancer therapy.

The following embodiments and aspects thereof are described andillustrated in conjunction with compositions and methods which are meantto be exemplary and illustrative, not limiting in scope.

We provide an assay for selecting a therapy for a subject having cancer,and optionally administering the therapy, the assay comprising:subjecting a sample comprising a cancer cell taken from the subject toan analysis for BLM and FANCI expression; comparing the BLM and FANCIexpression to a reference value; and selecting a platinum-comprisingcancer therapy for the subject when the BLM and FANCI expression isincreased compared to the reference value based on the recognition thatplatinum-comprising cancer therapy is effective in subjects whose cancerhas increased expression of BLM and FANCI, or selecting anon-platinum-comprising cancer therapy for the subject when the BLM andFANCI expression is not increased compared to the reference value basedon the recognition that platinum-comprising cancer therapy is noteffective in subjects whose cancer does not have increased BLM and FANCIexpression compared to the reference value.

The assay may further comprise assaying the BRCA1 and/or BRCA2 status ofthe subject; and selecting the platinum-comprising cancer therapy forthe subject when the subject is negative for BRCA1 and/or BRCA2mutations, and the BLM and FANCI expression is increased compared to thereference value based on the recognition that platinum-comprising cancertherapy is effective in subjects whose cancer has increased expressionof BLM and FANCI and who are negative for BRCA1 and/or BRCA2 mutations.

In some aspects of all the embodiments of the invention, the subject isknown to be or is determined to be negative for BRCA1 and/or BRCA2mutations.

In some aspects of all the embodiments of the invention, the assayfurther comprises assaying the estrogen receptor (ER), progesteronereceptor (PgR), and HER2 receptor status of the subject's cancer; andselecting the platinum-comprising cancer therapy for the subject whenthe subject's cancer does not express a detectable quantity of ER, PgR,and HER2 receptor, and when the BLM and FANCI expression is increasedcompared to the reference value based on the recognition thatplatinum-comprising cancer therapy is effective in subjects whose cancerhas increased expression of BLM and FANCI and whose cancer does notexpress a detectable quantity of ER, PgR, and HER2 receptor.

In some aspects of all the embodiments of the invention, the subject'scancer or cancer cell is known to not or is determined to not express adetectable quantity of ER, PgR, and HER2 receptor.

In some aspects of all the embodiments of the invention, the assayfurther comprises administering the selected therapy to the subject.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least BRCA1 gene expression in the cancer cell.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least one housekeeping gene expression in thecancer cell.

We also provide a method for selecting platinum-comprising therapy for asubject having cancer, and optionally administering theplatinum-comprising therapy, the method comprising: subjecting a samplecomprising a cancer cell taken from the subject to an analysis for BLMand FANCI expression; detecting the BLM and FANCI expression in thesample compared to a reference value; and electing a platinum-comprisingcancer therapy for the subject when the BLM and FANCI expressioncompared to a reference value is increased based on the recognition thatplatinum-comprising cancer therapy is effective in patients whose cancerhas increased BLM and FANCI expression compared to the reference value.

In some aspects of all the embodiments of the invention, the methodfurther comprises administering to the subject the platinum-comprisingcancer therapy when the platinum-comprising cancer therapy is selected.One can further select a therapy other than platinum-comprising therapywhen it is determined using the assay that the cancer is not likelyresponsive to platinum-comprising therapy.

In some aspects of all the embodiments of the invention, the subject isknown to be or is determined to be negative for BRCA1 and/or BRCA2mutations.

In some aspects of all the embodiments of the invention, the subject'scancer or cancer cell is known to not or determined to not express adetectable quantity of ER, PgR, and HER2 receptor.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least BRCA1 gene expression in the cancer cell.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least one housekeeping gene expression in thecancer cell.

In some aspects of all the embodiments of the invention, thehousekeeping gene is selected from beta-actin, GAPDH, RPLP0, GUS, TFRCand any combination thereof.

In some aspects of all the embodiments of the invention, thehousekeeping gene is RPLP0, and the BLM and/or FANCI expression isincreased by at least six-fold.

We further provide a method for selecting a non-platinum-comprisingtherapy, and optionally administering the non-platinum-comprisingtherapy, for a subject having cancer comprising: subjecting a samplecomprising a cancer cell taken from the subject to an analysis for BLMand FANCI expression; detecting the BLM and FANCI expression in thesample compared to a reference value; and selecting thenon-platinum-comprising cancer therapy for the subject when the BLM andFANCI expression compared to the reference value is not increased basedon the recognition that non-platinum-comprising cancer therapy iseffective in patients whose cancer does not have increased geneexpression of BLM and FANCI compared to the reference value.

In some aspects of all the embodiments of the invention, the methodfurther comprises administering to the subject thenon-platinum-comprising cancer therapy when non-platinum-comprisingcancer therapy is selected.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least BRCA1 gene expression in the cancer cell.

In some aspects of all the embodiments of the invention, the referencevalue is based on at least one housekeeping gene expression in thecancer cell.

We provide an assay for selecting a therapy for a subject having cancer,comprising: subjecting a sample comprising a cancer cell taken from thesubject to an analysis for BLM and FANCI expression; comparing the BLMand FANCI expression to a reference value; and selecting ananthracycline-comprising cancer therapy for the subject when the BLM andFANCI expression is increased compared to a reference value based on therecognition that anthracycline-comprising cancer therapy is effective insubjects whose cancer has increased expression of BLM and FANCI, orselecting a non-anthracycline-comprising cancer therapy for the subjectwhen the BLM and FANCI expression is not increased compared to areference value based on the recognition that anthracycline-comprisingcancer therapy is not effective in subjects whose cancer does not haveincreased BLM expression compared to a reference value.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We provide a method for selecting an anthracycline-comprising cancertherapy for a subject having cancer and determined to be negative forBRCA1 and/or BRCA2 mutations, comprising: subjecting a sample comprisinga cancer cell taken from the subject to an analysis for BLM and FANCIexpression; comparing the BLM and FANCI expression to a reference value;and selecting the anthracycline-compri sing cancer therapy for thesubject when the BLM and FANCI expression compared to the referencevalue is increased based on the recognition thatanthracycline-comprising cancer therapy is effective in patients whosecancer has increased expression of BLM and FANCI compared to thereference value.

In some aspects of all the embodiments of the invention, wherein thereference value is BRCA1 expression in the sample, and the BLM and/orFANCI expression is increased by at least two-fold compared to BRCA1expression.

We further provide a method of treating cancer in a human subject,comprising: detecting BLM and FANCI expression in a sample comprising acancer cell taken from the human subject; and comparing the BLM andFANCI expression to a reference value; and administering aplatinum-comprising cancer therapy to the human subject wherein anincrease of BLM and FANCI expression compared to the reference value isdetected.

In some aspects of all the embodiments of the invention, the humansubject's cancer or cancer cell is known to not or is determined to notexpress detectable quantities of estrogen receptor (ER), progesteronereceptor (PgR) and HER2 receptor.

In some aspects of all the embodiments of the invention, the cancer isselected from breast, ovarian, and lung cancers.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

In some aspects of all the embodiments of the invention, the referencevalue is based on BRCA1 gene expression in the cancer cell.

In some aspects of all the embodiments of the invention, the referencevalue is based on a housekeeping gene expression in the cancer cell.

We provide method of treating cancer in a human subject, comprising:detecting BLM and FANCI expression in a sample comprising a cancer celltaken from the human subject; and comparing the BLM and FANCI expressionto a reference value; and administering an anthracycline-comprisingcancer therapy to the human subject wherein an increase of BLM and FANCIexpression compared to the reference value is detected.

In some aspects of all the embodiments of the invention, the humansubject's cancer or cancer cell is known to not or is determined to notto express detectable quantities of estrogen receptor (ER), progesteronereceptor (PgR) and HER2 receptor.

In some aspects of all the embodiments of the invention, the cancer isselected from breast, ovarian, and lung cancers.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

In some aspects of all the embodiments of the invention, the referencevalue is based on BRCA1 gene expression in the cancer cell.

In some aspects of all the embodiments of the invention, the referencevalue is based on a housekeeping gene expression in the cancer cell.

We provide a method for assessing responsiveness of a cancer cell tocancer therapy, comprising: assaying, in a cancer cell or mRNA derivedtherefrom, BLM and FANCI expression; and comparing said BLM and FANCIexpression to a reference value, wherein the cancer cell is assessed asresponsive to a platinum-comprising therapy if the BLM and FANCIexpression is increased compared to the reference value, or wherein thecancer cell is assessed as poorly or not responsive toplatinum-comprising cancer therapy cancer if the BLM and FANCIexpression is not increased.

In some aspects of all the embodiments of the invention, the step ofassaying comprises: contacting the cancer cell or mRNA derived therefromwith at least one detectably labeled probe capable of specificallybinding to BLM mRNA, at least one detectably probe capable ofspecifically binding to FANCI, at least one detectably labeled probecapable of specifically binding to BRCA1 and/or at least onehousekeeping gene; and measuring the expression of BLM and FANCIcompared to the BRCA1 and/or the at least one housekeeping gene.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We provide a method of predicting a cancer patient's response to acancer treatment regimen comprising platinum or anthracycline,comprising: determining, in a cancer cell from the cancer patient, BLMand FANCI expression; and correlating the expression to a referencevalue, wherein when the expression is increased the patient is predictedto respond well to a cancer treatment regimen comprising platinum oranthracycline.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We also provide a method of predicting a cancer patient's response to acancer treatment regimen comprising platinum or anthracycline,comprising: determining, in a cancer cell or mRNA derived therefrom fromsaid cancer patient, BLM and FANCI expression; and correlating theexpression to a reference value, wherein when the expression is notincreased the patient is predicted to respond poorly to a cancertreatment regimen comprising platinum or anthracycline.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We provide a method of treating cancer, comprising: assaying, in acancer cell from a cancer patient or mRNA obtained therefrom, the BLMand FANCI expression compared to a reference value; and administering tothe cancer patient a cancer treatment regimen comprising platinum oranthracycline if the BLM and FANCI expression is increased compared tothe reference value.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We also provide a use of platinum comprising cancer therapy for treatinga cancer patient that has been determined to have a tumor comprisingcancer cells wherein BLM and FANCI expression is increased compared to areference value.

In some aspects of all the embodiments of the invention, the cancerpatient has been determined to be negative for BRCA1 and/or BRCA2mutations.

In some aspects of all the embodiments of the invention, the cancerpatient's cancer or cancer cell is known to not or is determined to notexpress detectable quantities of estrogen receptor (ER), progesteronereceptor (PgR) and HER2 receptor.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression in the sample, and the BLM and/or FANCIexpression is increased by at least two-fold compared to BRCA1expression.

We provide a system for determining responsiveness of a cancer cell toplatinum-comprising therapy from a cancer cell of a cancer patient,comprising: a sample analyzer configured to produce a signal for themRNA from each one of BLM and FANCI from a cancer cell sample of acancer patient; and a computer sub-system programmed to calculate, basedon the mRNA whether the signal is greater or not than a reference value.

In some aspects of all the embodiments of the invention, said computersub-system is programmed to compare the mRNA to determine a likelihoodof responsiveness of said cancer cell to platinum-comprising cancertherapy based on an algorithm that classifies the patient as likely torespond to a platinum-comprising therapy if the BLM and FANCI expressionis increased and as unlikely to respond to the platinum-comprisingtherapy if the BLM and FANCI expression is not increased; or alikelihood of responsiveness of said cancer cell toanthracycline-comprising cancer therapy based on an algorithm thatclassifies the patient as likely to respond to aanthracycline-comprising therapy if the BLM and FANCI expression isincreased and as unlikely to respond to the anthracycline-comprisingtherapy if the BLM and FANCI expression is not increased.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least two-fold compared to BRCA1 expression.

We provide a computer program product embodied in a computer readablemedium that, when executing on a computer, performs steps comprising:detecting the BLM and FANCI gene expression in sample comprising acancer cell from a cancer patient; and comparing the BLM and FANCIexpression to a reference value.

In some aspects of all the embodiments of the invention, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least two-fold compared to BRCA1 expression.

We provide a diagnostic kit for detecting a likelihood of a cancerpatient to respond to platinum- or anthracycline-comprising comprisingcancer therapy, comprising: no more than 10 probes comprising acombination of detectably labeled probes or primers for BLM and FANCI,and optionally for BRCA1 and/or at least one housekeeping gene; and thecomputer program product of Claim 59.

We provide use of a plurality of oligonucleotides comprising no morethan 10 oligonucleotides capable of hybridizing to BLM and FANCI, andoptionally to BRCA1 and/or at least one housekeeping gene, in adiagnostic kit for determining an increased likelihood that a cancerpatient will respond to cancer treatment regimen comprising a platinumand/or anthracycline.

In some aspects of all the embodiments of the invention, saidanthracycline is epirubincin or doxorubicin.

In some aspects of all the embodiments of the invention, said platinumcomprising cancer therapy comprises cisplatinum orcis-diamminedichloroplatinum, phenanthriplatin, carboplatin,oxaliplatin, or a platinum complex that is activated by ultraviolet Alight.

We provide an assay for selecting a therapy for a subject having cancer,and optionally administering the therapy, the assay comprising: assayinga sample comprising a cancer cell taken from the subject for achromosome 15q26 copy number; comparing the chromosome 15q26 copy numberto a reference value; and selecting a platinum-comprising cancer therapyfor the subject if there is a chromosome 15q26 copy number gain comparedto the reference value, or selecting a non-platinum-comprising cancertherapy for the subject if there is not a chromosome 15q26 copy numbergain, or if there is a chromosome 15q26 copy number loss.

In some aspects of all the embodiments of the invention, the assayfurther comprises: assaying the BRCA1 and/or BRCA2 status of thesubject; and selecting the platinum-comprising cancer therapy for thesubject when the subject is negative for BRCA1 and/or BRCA2 mutations,and there is a chromosome 15q26 copy number gain based on therecognition that platinum-comprising cancer therapy is effective insubjects who have a chromosome 15q26 copy number gain who are negativefor BRCA1 and/or BRCA2 mutations.

In some aspects of all the embodiments of the invention, the subject isknown to be or is determined to be negative for BRCA1 and/or BRCA2mutations.

In some aspects of all the embodiments of the invention, the assayfurther comprises: assaying the estrogen receptor (ER), progesteronereceptor (PgR), and HER2 receptor status of the subject's cancer; andselecting the platinum-comprising cancer therapy for the subject whenthe subject's cancer does not express a detectable quantity of ER, PgR,and HER2 receptor, and when there is a chromosome 15q26 copy number gainbased on the recognition that platinum-comprising cancer therapy iseffective in subjects who have a chromosome 15q26 copy number gain andwhose cancer does not express a detectable quantity of ER, PgR, and HER2receptor.

In some aspects of all the embodiments of the invention, the subject'scancer or cancer cell is known to not or is determined to not express adetectable quantity of ER, PgR, and HER2 receptor.

In some aspects of all the embodiments of the invention, the assayfurther comprises administering the selected therapy to the subject.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide an assay for selecting a therapy for a subject having cancer,and optionally administering the therapy, the assay comprising: assayinga sample comprising a cancer cell taken from the subject for achromosome 15q26 copy number; comparing the chromosome 15q26 copy numberto a reference value; and selecting an anthracycline-comprising cancertherapy for the subject if there is a chromosome 15q26 copy number gaincompared to the reference value, or selecting anon-anthracycline-comprising cancer therapy for the subject if there isnot a chromosome 15q26 copy number gain, or if there is a chromosome15q26 copy number loss.

In some aspects of all the embodiments of the invention, the assayfurther comprises: assaying the BRCA1 and/or BRCA2 status of thesubject; and selecting the anthracycline-comprising cancer therapy forthe subject when the subject is negative for BRCA1 and/or BRCA2mutations, and there is a chromosome 15q26 copy number gain based on therecognition that anthracycline-comprising cancer therapy is effective insubjects who have a chromosome 15q26 copy number gain who are negativefor BRCA1 and/or BRCA2 mutations.

In some aspects of all the embodiments of the invention, the subject isknown to be or is determined to be negative for BRCA1 and/or BRCA2mutations.

In some aspects of all the embodiments of the invention, the assayfurther comprises assaying the estrogen receptor (ER), progesteronereceptor (PgR), and HER2 receptor status of the subject's cancer; andselecting the anthracycline-comprising cancer therapy for the subjectwhen the subject's cancer does not express a detectable quantity of ER,PgR, and HER2 receptor, and when there is a chromosome 15q26 copy numbergain based on the recognition that anthracycline-comprising cancertherapy is effective in subjects who have a chromosome 15q26 copy numbergain and whose cancer does not express a detectable quantity of ER, PgR,and HER2 receptor.

In some aspects of all the embodiments of the invention, the subject'scancer or cancer cell is known to not or is determined to not express adetectable quantity of ER, PgR, and HER2 receptor.

In some aspects of all the embodiments of the invention, the assayfurther comprises administering the selected therapy to the subject.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide a method of treating cancer in a human subject, comprising:detecting a chromosome 15q26 copy number in a sample comprising a cancercell taken from the subject; comparing the chromosome 15q26 copy numberto a reference value; and administering an platinum-comprising cancertherapy for the subject if there is a chromosome 15q26 copy number gaincompared to the reference value, or administering anon-platinum-comprising cancer therapy for the subject if there is not achromosome 15q26 copy number gain, or if there is a chromosome 15q26copy number loss.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

In some aspects of all the embodiments of the invention, the subject'scancer is known to not express a detectable quantity of ER, PgR, andHER2 receptor.

We provide a method of treating cancer in a human subject, comprising:detecting a chromosome 15q26 copy number in a sample comprising a cancercell taken from the subject; comparing the chromosome 15q26 copy numberto a reference value; and administering an anthracycline-comprisingcancer therapy for the subject if there is a chromosome 15q26 copynumber gain compared to the reference value, or administering anon-anthracycline-comprising cancer therapy for the subject if there isnot a chromosome 15q26 copy number gain, or if there is a chromosome15q26 copy number loss.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

In some aspects of all the embodiments of the invention, the subject'scancer or cancer cell is known to not or is determined to not express adetectable quantity of ER, PgR, and HER2 receptor.

We provide a method for assessing responsiveness of a cancer cell to acancer therapy, and optionally administering the cancer therapy,comprising: assaying a sample comprising a cancer cell taken from thesubject for a chromosome 15q26 copy number; and comparing the chromosome15q26 copy number to a reference value, wherein the cancer cell isassessed as responsive to a platinum-comprising therapy if there is achromosome 15q26 copy number gain compared to the reference value, orwherein the cancer cell is assessed as poorly or not responsive toplatinum-comprising cancer therapy cancer if there is not a chromosome15q26 copy number gain or if there is a chromosome 15q26 copy numberloss.

In some aspects of all the embodiments of the invention, the referencevalue is copy number of chromosome 15.

In some aspects of all the embodiments of the invention, the cancer isselected from breast cancer, ovarian cancer and lung cancer.

In some aspects of all the embodiments of the invention, the methodfurther comprises administering the platinum-comprising therapy if thereis a chromosome 15q26 copy number gain.

We provide a method of predicting a cancer patient's response to acancer treatment regimen comprising platinum or anthracycline,comprising: determining, in a cancer cell from the cancer patient,chromosome 15q26 copy number; and correlating the chromosome 15q26 copynumber to a reference value, wherein when there is a chromosome 15q26copy number gain, the patient is predicted to respond well to a cancertreatment comprising platinum or anthracycline, or wherein when there isnot a chromosome 15q26 copy number gain or a chromosome 15q26 copynumber loss, the patient is predicted respond poorly to a cancertreatment comprising platinum or anthracycline.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide use of platinum comprising cancer therapy for treating acancer patient that has been determined to have a tumor comprisingcancer cells wherein a chromosome 15q26 copy gain is detected comparedto a reference value.

In some aspects of all the embodiments of the invention, the cancerpatient is known to be or is determined to be negative for BRCA1 and/orBRCA2 mutations.

In some aspects of all the embodiments of the invention, the cancerpatient's cancer or cancer cell is known to not or is determined to notexpress detectable quantities of estrogen receptor (ER), progesteronereceptor (PgR) and HER2 receptor.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide a system for determining responsiveness of a cancer cell toplatinum-comprising therapy from a cancer cell of a cancer patient,comprising: a sample analyzer configured to produce a signal forchromosome 15q26 copy number from a cancer cell sample of a cancerpatient; and a computer sub-system programmed to calculate, based on themRNA whether the signal is greater or not than a reference value.

In some aspects of all the embodiments of the invention, said computersub-system is programmed to compare the mRNA to determine a likelihoodof responsiveness of said cancer cell to platinum-comprising cancertherapy and/or or a anthracycline-comprising cancer therapy based on analgorithm that classifies the patient as likely to respond to aplatinum-comprising therapy if there is a chromosome 15q26 copy numbergain and as unlikely to respond to the platinum-comprising therapy ifthere is not a chromosome 15q26 copy number gain or if there is achromosome 15q26 copy number loss.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide a computer program product embodied in a computer readablemedium that, when executing on a computer, performs steps comprising:detecting chromosome 15q26 copy number in sample comprising a cancercell from a cancer patient; and comparing the chromosome 15q26 copynumber to a reference value.

In some aspects of all the embodiments of the invention, the referencevalue is chromosome 15 centromere copy number in the sample.

We provide a diagnostic kit for detecting a likelihood of a cancerpatient to respond to platinum- or anthracycline-comprising cancertherapy, comprising: no more than 10 probes comprising a combination ofdetectably labeled probes or primers for chromosome 15q26, andoptionally for chromosome 15 centromere; and a computer program asdescribed herein.

We provide us of a plurality of oligonucleotides comprising no more than10 oligonucleotides capable of hybridizing to chromosome 15q26, andoptionally for chromosome 15 centromere, in a diagnostic kit fordetermining an increased likelihood that a cancer patient will respondto cancer treatment regimen comprising a platinum and/or anthracycline.

In some aspects of all the embodiments of the invention, saidanthracycline is epirubincin or doxorubicin.

In some aspects of all the embodiments of the invention, said platinumcomprising cancer therapy comprises cisplatinum orcis-diamminedichloroplatinum, phenanthriplatin, carboplatin,oxaliplatin, or a platinum complex that is activated by ultraviolet Alight.

Other features and advantages of the invention will become apparent fromthe following detailed description, taken in conjunction with theaccompanying drawings, which illustrate, by way of example, variousfeatures of embodiments of the invention.

BRIEF DESCRIPTION OF THE FIGURES

This patent or application file contains at least one drawing executedin color. Copies of this patent or patent application publication withcolor drawings will be provided by the Office upon request and paymentof the necessary fee.

Exemplary embodiments are illustrated in referenced figures. It isintended that the embodiments and figures disclosed herein are to beconsidered illustrative rather than restrictive.

FIGS. 1A and 1B show that GISTIC identifies 169 chromosomal regions aseither gained or lost. Several contained genes with significantlydifferent copy number between sensitive and resistant cases. FIG. 1Ashows data relating to the Cisplatin-1 clinical trial. FIG. 1B showsdata relating to the Cisplatin-2 clinical trial.

FIG. 2 shows a 10 MB region with 59 genes on chr. 15q26.1-2 showedsignificant gain in sensitive samples.

FIG. 3 shows correlation between copy number and mRNA expression, Geneson 15q26.1-2. 23 genes show significant correlation.

FIG. 4 depicts leave-one-out analysis of gene expression data.

FIGS. 5A-5B shows that expression of BLM and FANCI is only associatedwith response to carboplatin, but not paclitaxel in OVO1. (FIG. 5A) BLMexpression; (FIG. 5B) FANCI Expression. Ahmed et al., Cancer Cell 2007.

FIGS. 6A-6B depicts expression of BLM or FANCI is not associated withresponse to multi-agent chemotherapy regimens in triple negative breastcancer (TNBC). (FIG. 6A) BLM expression; (FIG. 6B) FANCI Expression.¹Hess et al., JCO 2006; Popovici et al.; ²Breast Cancer Res 2010; ³Andréet al., Clin Cancer Res 2009.

FIG. 7 shows that BLM is also associated with response to single agentepirubicin. TOP trial, single agent epirubicin in ER-negative breastcancer. ¹Desmedt et al., JCO 2011.

FIG. 8 depicts repair of cisplatin induced damage.

FIG. 9 depicts the metaphase spread, BRCA1 knock-out in MEFs. BRCA1 isan essential part of the homologous repair system. BRCA1 knock out causehigh levels of quadrahelical chromosomes, which is a prime substrate forthe Bloom helicase. Gain of BLM is a possible compensation mechanism fordeficient HR. Silver D P et al, Cell 2007.

FIGS. 10A-10B show gene signatures. FIG. 10A shows receiver operatingcharacteristic curves showing the ability of the BRCA1-BLM-FANCI RNA3-gene signature to predict for response to cisplatin in the twocisplatin trials. FIG. 10B shows ROC curves showing the ability ofnumber of telomeric allelic imbalance (NtAI)+3-gene mRNA signature topredict for sensitivity to cisplatin in the combined trials.

FIG. 11 depicts ROC analysis of 3 gene signature to determine cisplatinsensitivity in cisplatin 2 trial. Blue: all cases; red; BRCA normalcases only.

FIG. 12 depicts functional modules of various embodiments of theinvention.

FIG. 13 depicts survival time with Kaplan-Meier plot, showing over-allsurvival of patients from the TCGA squamous cell lung cancer cohort,split by the median of the three gene signature calculated as the ratioof BRCA1 expression over the mean of FANI and BLM expression.

FIG. 14 shows the BLM+FANCI/BRCA1 signature. The Cisplatin-2 trial,separating resistant (MP 1-2-3) from sensitive (MP 4-5) cases isoptimized for qPCR data. Blue line is based on all samples, while red isbased on wtBRCA1. The optimum ratio is calculated by ROC curve, andshows an optimum ratio of 5.5 for all cases, on a log 2 scale. Inun-logged values, this is equivalent of 45 fold.

FIG. 15 shows BLM/BRCA1 signature. The Cisplatin-2 trial, separatingresistant (MP 1-2-3) from sensitive (MP 4-5) cases is optimized for qPCRdata. The optimum ratio is 7.5 for all cases, on a log 2 scale, which isequivalent of 180 fold or 7.5 cycles on a PCR machine. This is a verylarge difference.

FIG. 16 shows FANCI/BRCA1 signature. The Cisplatin-2 trial, separatingresistant (MP 1-2-3) from sensitive (MP 4-5) cases is optimized for qPCRdata. The optimum ratio is 5.1 for all cases, on a log 2 scale, which isequivalent of 34 fold.

FIG. 17 shows the BRCA1/RPLP0 signature. BRCA1 is compared to ahousekeeping gene, RPLP0. The optimum ratio here is −14 for all cases,on a log 2 scale, which is approximately equivalent to 1/1600, or 14cycles on a PCR machine. This is a very large difference, but HK genesare expressed in very high numbers.

FIG. 18 shows BLM/RPLP0 signature. BLM is compared to a housekeepinggene, RPLP0 The optimum ratio is higher, and separation ofsensitive/resistant cases is good.

FIG. 19 shows FANCI/RPLP0 signature. FANCI is compared to a housekeepinggene, RPLP0. The optimum ratio is higher than BRCA1 alone.

FIGS. 20A and 20B show how the expression of each of the three geneslooks like in a large cohort of breast cancer patients from the TCGA,and how their ratios is to RPLP0 and BRCA1. These patients were nottreated with platinum. This was focused on DNBC cases (ER/HER2negative), and the normal breast samples. The ratio is much lower thanusing PCR data, yet there still appear to be a clear increase in somecases. The normal samples have lower BLM and BRCA1 expression, but thatthe ratio between these is inversed, with higher BRCA1 than BLM,probably reflecting the normal balance between these genes. FIG. 20Ashows the expression of ESR1, BLM, ERBB2, FANCI, BRCA1, and RPLP0 inDNBC, estrogen receptor negative (ER), and HER2 receptor negative breastcancer patients and in patients with metastases compared to normalbreast samples. FIG. 20B shows data relating to (i) the 3-genesignature, (ii) BRCA1/RPLP0 ratio, (iii) BLM/BRCA1 ratios, (iv)BLMIRPLP0 ratios, (v) FANCI/BRCA1 ratios, and (vi) FANCI/RPLP0 ratios inthe same cohorts as FIG. 20A.

DETAILED DESCRIPTION

All references cited herein are incorporated by reference in theirentirety as though fully set forth. Unless defined otherwise, technicaland scientific terms used herein have the same meaning as commonlyunderstood by one of ordinary skill in the art to which this inventionbelongs. Singleton et al., Dictionary of Microbiology and MolecularBiology 3^(rd) ed., J. Wiley & Sons (New York, N.Y. 2001); March,Advanced Organic Chemistry Reactions, Mechanisms and Structure 5^(th)ed., J. Wiley & Sons (New York, N.Y. 2001); and Sambrook and Russel,Molecular Cloning: A Laboratory Manual 3rd ed., Cold Spring HarborLaboratory Press (Cold Spring Harbor, N.Y. 2001), provide one skilled inthe art with a general guide to many of the terms used in the presentapplication. For references on how to prepare antibodies, see D. Lane,Antibodies: A Laboratory Manual (Cold Spring Harbor Press, Cold SpringHarbor N.Y., 1988); Kohler and Milstein, (1976) Eur. J. Immunol. 6: 511;Queen et al. U.S. Pat. No. 5,585,089; and Riechmann et al., Nature 332:323 (1988).

One skilled in the art will recognize many methods and materials similaror equivalent to those described herein, which could be used in thepractice of the present invention. Indeed, the present invention is inno way limited to the methods and materials described.

To investigate whether specific genomic aberrations may affect cancersensitivity to cisplatin, the inventors generated tumor DNA copy numberprofiles of 21 and 24 TNBC patients who received pre-operativecisplatin-based chemotherapy in two separate clinical trials. Using theGISTIC algorithm (1), the inventors found that only a single region onchromosome 15q26 showed consistent significant differential copy numberin responders versus non-responders, being preferentially lost innon-responders, but preferentially gained in responders in both trials.

To see if genes on 15q26 were associated with platinum sensitivity, theinventors acquired gene expression data from the cisplatin TNBC trial(2), and from the carboplatin-only arm of an ovarian cancer trial (3).The inventors then performed a leave-one-out analysis, and found 9 genessignificantly associated with platinum response in at least 75% of allrounds in both cohorts. These included BLM and FANCI located in the15q26 region, both showing higher expression in sensitive tumors, andknown to be involved in related DNA repair processes. To investigate ifBLM and FANCI were specifically associated with genotoxic chemotherapysensitivity, the inventors analyzed their expression in TNBCs from threeneoadjuvant trials of epirubicin alone (4) or taxane-containingcombination therapy (5, 6) and in ovarian cancers from the taxane-onlytreatment arm (3). In the epirubicin trial, BLM and FANCI expression wasagain significantly associated with increased sensitivity to therapy. Incontrast, there was no association between either BLM or FANCIexpression and TNBC response to the taxane-containing regimen or ovariancancer response to single agent taxane treatment. These data suggestthat high expression of BLM and FANCI are associated with improvedresponse to DNA damaging agents, but not with response to other types ofchemotherapeutics. Furthermore, it suggests that the patientsubpopulations that respond to drugs such as anthracyclines and taxanesare not overlapping, and that it will therefore be difficult to robustlyidentify predictors of single agent response based on multi-drug trials.

While not wishing to be bound by any particular theory, the inventorsbelieve that FANCI and BLM functions in multiple DNA repair processes;increased FANCI and BLM is associated with response toplatinum-comprising therapy and anthracycline-comprising therapy; lowcopy gain might be a compensatory mechanism of HR deficient cells,trying to rescue some DNA repair capacity; and if so, FANCI/BLMexpression is a marker for DNA repair deficiency, and increasedsensitivity to genotoxic chemotherapy drugs, such as platinum-comprisingtherapy and anthracycline-comprising therapy.

Therefore, while the cancers specifically investigated for theirresponses in the particular studies, such as breast cancer, such astriple negative breast cancer, ovarian cancer and lung cancer,Applicants believe that the finding of the association between increasedFANCI and BLM expression and responsiveness to platinum-comprisingtherapy and anthracycline-comprising therapy is applicable to mostcancers.

The present invention is based, at least in part, on these findings, andthose further described herein and in the figures and examples.

Selecting Therapy

Various embodiments provide for assays, methods and systems forselecting an appropriate therapy for a subject based on an analysis ofthe subject's BLM and FANCI expression, or based on the subject's 15q26copy number.

In various embodiments, the invention provide for an assay for selectinga therapy, and optionally administering the therapy, for a subjecthaving cancer, the assay comprising: subjecting a sample comprising acancer cell taken from the subject to an analysis for BLM and FANCIexpression; comparing the BLM and FANCI expression to a reference value;and selecting a platinum-comprising cancer therapy for the subject whenthe BLM and FANCI expression is increased compared to the referencevalue based on the recognition that platinum-comprising cancer therapyis effective in subjects whose cancer has increased expression of BLMand FANCI, or selecting a non-platinum-comprising cancer therapy for thesubject when the BLM and FANCI expression is not increased compared tothe reference value based on the recognition that platinum-comprisingcancer therapy is not effective in subjects whose cancer does not haveincreased BLM and FANCI expression compared to the reference value.

In various embodiments, the assay further comprises: assaying the BRCA1and/or BRCA2 status of the subject; and selecting theplatinum-comprising cancer therapy for the subject when the subject isnegative for BRCA1 and/or BRCA2 mutations, and the BLM and FANCIexpression is increased compared to the reference value based on therecognition that platinum-comprising cancer therapy is effective insubjects whose cancer has increased expression of BLM and FANCI and whoare negative for BRCA1 and/or BRCA2 mutations. In various embodiments,the subject is known to be or is determined to be negative for BRCA1and/or BRCA2 mutations. The determination can be made before,concurrently with, or after the analysis for BLM and FANCI expression.

In some aspects of all the embodiments of the invention, a mutation thatinactivates BRCA2 is highly predictive of response.

In various embodiments, the assay further comprises: assaying theestrogen receptor (ER), progesterone receptor (PgR), and HER2 receptorstatus of the subject's cancer; and selecting the platinum-comprisingcancer therapy for the subject when the subject's cancer does notexpress a detectable quantity of ER, PgR, and HER2 receptor, and whenthe BLM and FANCI expression is increased compared to the referencevalue based on the recognition that platinum-comprising cancer therapyis effective in subjects whose cancer has increased expression of BLMand FANCI and whose cancer does not express a detectable quantity of ER,PgR, and HER2 receptor. In various embodiments, the subject's cancer orcancer cell is known to not or is determined to not express a detectablequantity of ER, PgR, and HER2 receptor. The determination can be madebefore, concurrently with, or after analysis for BLM and FANCIexpression.

In various embodiments, the assay further comprises administering theselected therapy to the subject.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3-fold, 4-fold,5-fold, or 6-fod, 10-20 fold, 20-50 fold or higher, depending on theexpression level of the gene used as a standard, such as one or morehousekeeping genes or BRCA1.

Typically, an increase in expression of at least 1.5 or at least 2 foldis considered as a cut-off point for increased expression if BRCA1 geneexpression is used as a standard. Thus, in certain embodiments, thereference value is BRCA1 expression, and the BLM and/or FANCI expressionis increased by at least two-fold compared to BRCA1 expression.

For example, in our examples, we calculated the ratios, and in cellsexpressing wild type BRCA1 (wtBRCA1) the ratio was around 6.6 forBLM+FANCI/BRCA1. Thus, is some aspects, the expression level can be over5, or over 6 or over 7 times that of BRCA1.

For analysis with qPCR, each of the analyzed genes is first normalizedto a housekeeping gene, such as RPLP0. For example, with 6 cycles ofPCT, we calculated the optimum for BRCA1/BLM/FANCI normalized to RPLP0,expression of which is typically very low. All values are log 2, whichmeans that a ratio of 6 reflects an amount of 64 times higher than thereference gene, namely RPLP0.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Examples of useful housekeepinggenes are described herein, e.g., in Table 1.

Various embodiments of the present invention provide for a method forselecting platinum-comprising therapy, and optionally administering theplatinum-comprising therapy, for a subject having cancer, comprising:subjecting a sample comprising a cancer cell taken from the subject toan analysis for BLM and FANCI expression; detecting the BLM and FANCIexpression in the sample compared to a reference value; and selecting aplatinum-comprising cancer therapy for the subject when the BLM andFANCI expression compared to a reference value is increased based on therecognition that platinum-comprising cancer therapy is effective inpatients whose cancer has increased BLM and FANCI expression compared tothe reference value.

In various embodiments, the method further comprises administering tothe subject the platinum-comprising cancer therapy when theplatinum-comprising cancer therapy is selected.

In various embodiments, the subject is known to be or is determined tobe negative for BRCA1 and/or BRCA2 mutations. The determination can bemade before, concurrently with, or after the analysis for BLM and FANCIexpression. In various embodiments, the subject's cancer or cancer cellis known to not or is determined to not express a detectable quantity ofER, PgR, and HER2 receptor. The determination can be made before,concurrently with, or after analysis for BLM and FANCI expression.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leastor about two-fold compared to BRCA1 expression. In certain embodiments,the BLM and/or FANCI expression is increased by at least or about 6-foldcompared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein.

In certain embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer.

Various embodiments of the present invention provide for a method forselecting a non-platinum-comprising therapy, and optionallyadministering the non-platinum-comprising therapy, for a subject havingcancer comprising: subjecting a sample comprising a cancer cell takenfrom the subject to an analysis for BLM and FANCI expression; detectingthe BLM and FANCI expression in the sample compared to a referencevalue; and selecting the non-platinum-comprising cancer therapy for thesubject when the BLM and FANCI expression compared to the referencevalue is not increased based on the recognition thatnon-platinum-comprising cancer therapy is effective in patients whosecancer does not have increased gene expression of BLM and FANCI comparedto the reference value.

In some aspects of all the embodiments of the invention a dual assayallowing analysis of both BLM and FANCI expression to be compared in thesame assay is used. The dual assay may be based on detecting RNA orprotein. The assay may be specific for the dual analysis of BLM andFANCI or may comprise reagents for assaying one, two, three or moreother biomolecules as well. In some aspects of all the embodiments ofthe invention the one other biomolecule is BRCA1.

In various embodiments, the method further comprises administering tothe subject the non-platinum-comprising cancer therapy whennon-platinum-comprising cancer therapy is selected.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Examples of housekeeping genes aredescribed herein although these genes are well known to one of ordinaryskill in the art.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer.

Various embodiments of the present invention provide for an assay forselecting a therapy for a subject having cancer, comprising: subjectinga sample comprising a cancer cell taken from the subject to an analysisfor BLM and FANCI expression; comparing the BLM and FANCI expression,optionally in a dual assay, to a reference value; and selecting ananthracycline-comprising cancer therapy for the subject when the BLM andFANCI expression is increased compared to a reference value based on therecognition that anthracycline-comprising cancer therapy is effective insubjects whose cancer has increased expression of BLM and FANCI, orselecting a non-anthracycline-comprising cancer therapy for the subjectwhen the BLM and FANCI expression is not increased compared to areference value based on the recognition that anthracycline-comprisingcancer therapy is not effective in subjects whose cancer does not haveincreased BLM expression compared to a reference value.

Various embodiments of the present invention provide for a method forselecting an anthracycline-comprising cancer therapy for a subjecthaving cancer and determined to be negative for BRCA1 and BRCA2mutations, comprising: subjecting a sample comprising a cancer celltaken from the subject to an analysis for BLM and FANCI expressioncomparing the BLM and FANCI expression to a reference value; andselecting the anthracycline-comprising cancer therapy for the subjectwhen the BLM and FANCI expression compared to the reference value isincreased based on the recognition that anthracycline-comprising cancertherapy is effective in patients whose cancer has increased expressionof BLM and FANCI compared to the reference value.

Various embodiments provide for an assay for selecting a therapy for asubject having cancer, and optionally administering the therapy, theassay comprising: assaying a sample comprising a cancer cell taken fromthe subject for a chromosome 15q26 copy number; comparing the chromosome15q26 copy number to a reference value; and selecting aplatinum-comprising cancer therapy for the subject if there is achromosome 15q26 copy number gain compared to the reference value, orselecting a non-platinum-comprising cancer therapy for the subject ifthere is not a chromosome 15q26 copy number gain, or if there is achromosome 15q26 copy number loss.

In various embodiments, the assay further comprises assaying the BRCA1and/or BRCA2 status of the subject; and selecting theplatinum-comprising cancer therapy for the subject when the subject isnegative for BRCA1 and/or BRCA2 mutations, and there is a chromosome15q26 copy number gain based on the recognition that platinum-comprisingcancer therapy is effective in subjects who have a chromosome 15q26 copynumber gain who are negative for BRCA1 and/or BRCA2 mutations. Invarious embodiments, the subject is known to be or is determined to benegative for BRCA1 and/or BRCA2 mutations. The determination can be madebefore, concurrently with, or after the analysis for BLM and FANCIexpression.

In various embodiments, the assay further comprises assaying theestrogen receptor (ER), progesterone receptor (PgR), and HER2 receptorstatus of the subject's cancer; and selecting the platinum-comprisingcancer therapy for the subject when the subject's cancer does notexpress a detectable quantity of ER, PgR, and HER2 receptor, and whenthere is a chromosome 15q26 copy number gain based on the recognitionthat platinum-comprising cancer therapy is effective in subjects whohave a chromosome 15q26 copy number gain and whose cancer does notexpress a detectable quantity of ER, PgR, and HER2 receptor. In variousembodiments, the subject's cancer or cancer cell is known to not or isdetermined to not express a detectable quantity of ER, PgR, and HER2receptor. The determination can be made before, concurrently with, orafter analysis for chromosome 15q26 copy number.

In various embodiments, the assay further comprises administering theselected therapy to the subject.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer.

In various embodiments, the reference value is chromosome 15 centromerecopy number.

Various embodiments of the present invention provide for an assay forselecting a therapy for a subject having cancer, and optionallyadministering the therapy, the assay comprising: assaying a samplecomprising a cancer cell taken from the subject for a chromosome 15q26copy number; comparing the chromosome 15q26 copy number to a referencevalue; and selecting an anthracycline-comprising cancer therapy for thesubject if there is a chromosome 15q26 copy number gain compared to thereference value, or selecting a non-anthracycline-comprising cancertherapy for the subject if there is not a chromosome 15q26 copy numbergain, or if there is a chromosome 15q26 copy number loss.

In various embodiments, the assay further comprises assaying the BRCA1and/or BRCA2 status of the subject; and selecting theanthracycline-comprising cancer therapy for the subject when the subjectis negative for BRCA1 and/or BRCA2 mutations, and there is a chromosome15q26 copy number gain based on the recognition thatanthracycline-comprising cancer therapy is effective in subjects whohave a chromosome 15q26 copy number gain and who are negative for BRCA1and/or BRCA2 mutations. In various embodiments, the subject is known tobe or is determined to be negative for BRCA1 and/or BRCA2 mutations. Insome aspects of all the embodiments of the invention, a mutation thatinactivates BRCA2 is highly predictive of response toplatinum-comprising cancer therapy. The determination can be madebefore, concurrently with, or after analysis for chromosome 15q26 copynumber.

In various embodiments, the assay further comprises assaying theestrogen receptor (ER), progesterone receptor (PgR), and HER2 receptorstatus of the subject's cancer; and selecting theanthracycline-comprising cancer therapy for the subject when thesubject's cancer does not express a detectable quantity of ER, PgR, andHER2 receptor, and when there is a chromosome 15q26 copy number gainbased on the recognition that anthracycline-comprising cancer therapy iseffective in subjects who have a chromosome 15q26 copy number gain andwhose cancer does not express a detectable quantity of ER, PgR, and HER2receptor. In various embodiments, the subject's cancer or cancer cell isknown to not or is determined to not express a detectable quantity ofER, PgR, and HER2 receptor. The determination can be made before,concurrently with, or after analysis for chromosome 15q26 copy number.

In various embodiments, the assay further comprises administering theselected therapy to the subject.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer.

In various embodiments, the reference value is chromosome 15 centromerecopy number.

Cancer Treatment

Various embodiments of the present invention provide for a method oftreating cancer in a human subject, comprising: detecting BLM and FANCIexpression in a sample comprising a cancer cell taken from the humansubject; and comparing the BLM and FANCI expression to a referencevalue; and administering a platinum-comprising cancer therapy to thehuman subject wherein an increase of BLM and FANCI expression comparedto the reference value is detected.

In various embodiments, the cancer is selected from breast, ovarian, andlung cancers.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein.

In certain embodiments, the human subject's cancer or cancer cell isknown to not or determined not to express detectable quantities ofestrogen receptor (ER), progesterone receptor (PgR) and HER2 receptor.The determination can be made before, concurrently with, or afteranalysis for chromosome 15q26 copy number.

Various embodiments of the present invention provide for a method oftreating cancer in a human subject, comprising: detecting BLM and FANCIexpression in a sample comprising a cancer cell taken from the humansubject; and comparing the BLM and FANCI expression to a referencevalue; and administering an anthracycline-comprising cancer therapy tothe human subject wherein an increase of BLM and FANCI expressioncompared to the reference value is detected.

In various embodiments, the human subject's cancer is known to not ordetermined to not express detectable quantities of estrogen receptor(ER), progesterone receptor (PgR) and HER2 receptor. The determinationcan be made before, concurrently with, or after analysis for chromosome15q26 copy number.

In various embodiments, the cancer is selected from breast, ovarian, andlung cancers.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein, e.g., in Table 1.

Various embodiments of the present invention provide for a method oftreating cancer, comprising: assaying, in a cancer cell from a cancerpatient or mRNA obtained therefrom, the BLM and FANCI expressioncompared to a reference value; and administering to the cancer patient acancer treatment regimen comprising platinum or anthracycline if the BLMand FANCI expression is increased compared to the reference value.

Various embodiments provide for a use of platinum comprising cancertherapy for treating a cancer patient that has been determined to have atumor comprising cancer cells wherein BLM and FANCI expression isincreased compared to a reference value.

In various embodiments, the cancer patient is known to be or isdetermined to be negative for BRCA1 and/or BRCA2 mutations. Thedetermination can be made before, concurrently with, or after theanalysis for BLM and FANCI expression. In certain embodiments, thecancer patient's cancer or cancer cell is known to not or is determinedto not express detectable quantities of estrogen receptor (ER),progesterone receptor (PgR) and HER2 receptor. The determination can bemade before, concurrently with, or after analysis of BLM and FANCIexpression.

Various embodiments of the present invention provide for a method oftreating cancer in a human subject whose cancer has increased BLM andFANCI expression, comprising: identifying the human subject whose cancerhas increased BLM and FANCI expression; and administering aplatinum-comprising cancer therapy or an anthracycline-comprisingtherapy to the human subject. In certain embodiments, the humansubject's cancer is known to not or is determined to not expressdetectable quantities of estrogen receptor (ER), progesterone receptor(PgR) and HER2 receptor. In various embodiments, the human subject isknown to be or is determined to be negative for BRCA1 and/or BRCA2mutations. These determinations can be made before, concurrently with,or after analysis of BLM and FANCI expression.

Various embodiments of the present invention provide for a method oftreating cancer in a human subject, comprising: detecting a chromosome15q26 copy number in a sample comprising a cancer cell taken from thesubject; comparing the chromosome 15q26 copy number to a referencevalue; and administering an platinum-comprising cancer therapy for thesubject if there is a chromosome 15q26 copy number gain compared to thereference value, or administering a non-platinum-comprising cancertherapy for the subject if there is not a chromosome 15q26 copy numbergain, or if there is a chromosome 15q26 copy number loss.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer. In various embodiments, the referencevalue is chromosome 15 centromere copy number. In various embodiments,the subject's cancer or cancer cell is known to not or is determined tonot express a detectable quantity of ER, PgR, and HER2 receptor. Thedetermination can be made before, concurrently with, or after analysisof chromosome 15q26 copy number.

Various embodiments of the present invention provide for a method oftreating cancer in a human subject, comprising: detecting a chromosome15q26 copy number in a sample comprising a cancer cell taken from thesubject; comparing the chromosome 15q26 copy number to a referencevalue; and administering an anthracycline-comprising cancer therapy forthe subject if there is a chromosome 15q26 copy number gain compared tothe reference value, or administering a non-anthracycline-compri singcancer therapy for the subject if there is not a chromosome 15q26 copynumber gain, or if there is a chromosome 15q26 copy number loss.

In various embodiments, the cancer is selected from breast cancer,ovarian cancer and lung cancer. In various embodiments, the referencevalue is chromosome 15 centromere copy number. In various embodiments,the subject's cancer or cancer cell is known to not or is determined tonot express a detectable quantity of ER, PgR, and HER2 receptor. Thedetermination can be made before, concurrently with, or after analysisof chromosome 15q26 copy number.

Assessing and Predicting Responsiveness to Cancer Therapy

Various embodiments of the present invention provide for a method forassessing responsiveness of a cancer cell to cancer therapy, comprising:assaying, in a cancer cell or mRNA derived therefrom, BLM and FANCIexpression; and comparing said BLM and FANCI expression to a referencevalue, wherein the cancer cell is assessed as responsive to aplatinum-comprising therapy if the BLM and FANCI expression is increasedcompared to the reference value, or wherein the cancer cell is assessedas poorly or not responsive to platinum-comprising cancer therapy cancerif the BLM and FANCI expression is not increased.

In various embodiments, the step of assaying comprises: contacting thecancer cell or mRNA derived therefrom with at least one detectablylabeled probe capable of specifically binding to BLM mRNA, at least onedetectably probe capable of specifically binding to FANCI, at least onedetectably labeled probe capable of specifically binding to BRCA1 and/orat least one housekeeping gene; and measuring the expression of BLM andFANCI compared to the BRCA1 and/or the at least one housekeeping gene.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein, e.g., in Table 1.

Various embodiments of the present invention provide for a method ofpredicting a cancer patient's response to a cancer treatment regimencomprising platinum or anthracycline, comprising: determining, in acancer cell from the cancer patient, BLM and FANCI expression; andcorrelating the expression to a reference value, wherein when theexpression is increased the patient is predicted to respond well to acancer treatment regimen comprising platinum or anthracycline.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein, e.g., in Table 1.

Various embodiments of the present invention provide for a method ofpredicting a cancer patient's response to a cancer treatment regimencomprising platinum or anthracycline, comprising: determining, in acancer cell or mRNA derived therefrom from said cancer patient, BLM andFANCI expression; and correlating the expression to a reference value,wherein when the expression is not increased the patient is predicted torespond poorly to a cancer treatment regimen comprising platinum oranthracycline.

In various embodiments, the reference value is based on BRCA1 geneexpression in the cancer cell. In various embodiments, the referencevalue is BRCA1 expression, and the BLM and/or FANCI expression isincreased by at least or about 10, 20, 30, 40, 50, 60, 70, 80, or 90%compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or 3-fold compared toBRCA1 expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leasttwo-fold compared to BRCA1 expression.

In various embodiments, the reference value is based on a housekeepinggene expression in the cancer cell. Housekeeping genes are describedherein.

Various embodiments provide for a method for assessing responsiveness ofa cancer cell to a cancer therapy, and optionally administering thecancer therapy, comprising: assaying a sample comprising a cancer celltaken from the subject for a chromosome 15q26 copy number; and comparingthe chromosome 15q26 copy number to a reference value, wherein thecancer cell is assessed as responsive to a platinum-comprising therapyif there is a chromosome 15q26 copy number gain compared to thereference value, or wherein the cancer cell is assessed as poorly or notresponsive to platinum-comprising cancer therapy cancer if there is nota chromosome 15q26 copy number gain or if there is a chromosome 15q26copy number loss.

In various embodiments, the reference value is chromosome 15 centromerecopy number. In various embodiments, the cancer is selected from breastcancer, ovarian cancer and lung cancer.

In various embodiments, the method further comprises administering theplatinum-comprising therapy if there is a chromosome 15q26 copy numbergain.

Various embodiments provide for a method of predicting a cancerpatient's response to a cancer treatment regimen comprising platinum oranthracycline, comprising: determining, in a cancer cell from the cancerpatient, chromosome 15q26 copy number; and correlating the chromosome15q26 copy number to a reference value, wherein when there is achromosome 15q26 copy number gain, the patient is predicted to respondwell to a cancer treatment comprising platinum or anthracycline, orwherein when there is not a chromosome 15q26 copy number gain or achromosome 15q26 copy number loss, the patient is predicted respondpoorly to a cancer treatment comprising platinum or anthracycline.

In various embodiments, the reference value is chromosome 15 centromerecopy number.

Various embodiments provide for the use of platinum comprising cancertherapy for treating a cancer patient that has been determined to have atumor comprising cancer cells wherein a chromosome 15q26 copy gain isdetected compared to a reference value. In various embodiments, cancerpatient is known to be or is determined to be negative for BRCA1 and/orBRCA2 mutations. The determination can be made before, concurrentlywith, or after the analysis for BLM and FANCI expression. In variousembodiments, the cancer patient is known to not or is determined to notexpress detectable quantities of estrogen receptor (ER), progesteronereceptor (PgR) and HER2 receptor. In various embodiments, the referencevalue is chromosome 15 centromere copy number.

Systems, Computers, Kits and Uses

Various embodiments of the present invention provide for a system fordetermining responsiveness of a cancer cell to platinum-comprisingtherapy from a cancer cell of a cancer patient, comprising: a sampleanalyzer configured to produce a signal for the mRNA from each one ofBLM and FANCI from a cancer cell sample of a cancer patient; and acomputer sub-system programmed to calculate, based on the mRNA whetherthe signal is greater or not than a reference value.

In various embodiments, said computer sub-system is programmed tocompare the mRNA to determine a likelihood of responsiveness of saidcancer cell to platinum-comprising cancer therapy based on an algorithmthat classifies the patient as likely to respond to aplatinum-comprising therapy if the BLM and FANCI expression is increasedand as unlikely to respond to the platinum-comprising therapy if the BLMand FANCI expression is not increased; or a likelihood of responsivenessof said cancer cell to anthracycline-comprising cancer therapy based onan algorithm that classifies the patient as likely to respond to aanthracycline-comprising therapy if the BLM and FANCI expression isincreased and as unlikely to respond to the anthracycline-comprisingtherapy if the BLM and FANCI expression is not increased.

Various embodiments of the present invention provide for a system fordetermining responsiveness of a cancer cell to platinum-comprisingtherapy from a cancer cell of a cancer patient, comprising: a sampleanalyzer configured to produce a signal for the protein from each one ofBLM and FANCI from a cancer cell sample of a cancer patient; and acomputer sub-system programmed to calculate, based on the proteinwhether the signal is greater or not than a reference value.

In various embodiments, said computer sub-system is programmed tocompare the protein to determine a likelihood of responsiveness of saidcancer cell to platinum-comprising cancer therapy based on an algorithmthat classifies the patient as likely to respond to aplatinum-comprising therapy if the BLM and FANCI expression is increasedand as unlikely to respond to the platinum-comprising therapy if the BLMand FANCI expression is not increased; or a likelihood of responsivenessof said cancer cell to anthracycline-comprising cancer therapy based onan algorithm that classifies the patient as likely to respond to aanthracycline-comprising therapy if the BLM and FANCI expression isincreased and as unlikely to respond to the anthracycline-comprisingtherapy if the BLM and FANCI expression is not increased.

Various embodiments of the present invention provide for a computerprogram product embodied in a computer readable medium that, whenexecuting on a computer, performs steps comprising: detecting the BLMand FANCI expression in sample comprising a cancer cell from a cancerpatient; and comparing the BLM and FANCI expression to a referencevalue.

Various embodiments of the present invention provide for a diagnostickit for detecting a likelihood of a cancer patient to respond toplatinum- or anthracycline-compri sing comprising cancer therapy,comprising: no more than 10 probes comprising a combination ofdetectably labeled probes or primers for BLM and FANCI, and optionallyfor BRCA1 and/or at least one housekeeping gene; and the computerprogram product.

Various embodiments of the present invention provide for the use of aplurality of oligonucleotides comprising no more than 10oligonucleotides capable of hybridizing to BLM and FANCI, and optionallyto BRCA1 and/or at least one housekeeping gene, in a diagnostic kit fordetermining an increased likelihood that a cancer patient will respondto cancer treatment regimen comprising a platinum and/or anthracycline.

Various embodiments provide for a system for determining responsivenessof a cancer cell to platinum-comprising therapy from a cancer cell of acancer patient, comprising: a sample analyzer configured to produce asignal for chromosome 15q26 copy number from a cancer cell sample of acancer patient; and a computer sub-system programmed to calculate, basedon the mRNA whether the signal is greater or not than a reference value.

In various embodiments, the computer sub-system is programmed to comparethe mRNA to determine a likelihood of responsiveness of said cancer cellto platinum-comprising cancer therapy and/or or aanthracycline-comprising cancer therapy based on an algorithm thatclassifies the patient as likely to respond to a platinum-comprisingtherapy if there is a chromosome 15q26 copy number gain and as unlikelyto respond to the platinum-comprising therapy if there is not achromosome 15q26 copy number gain or if there is a chromosome 15q26 copynumber loss. In various embodiments, the reference value is chromosome15 centromere copy number.

Various embodiments of the present invention provide for a computerprogram product embodied in a computer readable medium that, whenexecuting on a computer, performs steps comprising: detecting chromosome15q26 copy number in sample comprising a cancer cell from a cancerpatient; and comparing the chromosome 15q26 copy number to a referencevalue. In various embodiments, the reference value is chromosome 15centromere copy number.

Various embodiments of the present invention provide for a diagnostickit for detecting a likelihood of a cancer patient to respond toplatinum- or anthracycline-compri sing cancer therapy, comprising: nomore than 10 probes comprising a combination of detectably labeledprobes or primers for chromosome 15q26, and optionally for chromosome 15centromere; and the computer program product of described herein.

Various embodiments of the present invention provide for the use of aplurality of oligonucleotides comprising no more than 10oligonucleotides capable of hybridizing to chromosome 15q26, andoptionally for chromosome 15 centromere, in a diagnostic kit fordetermining an increased likelihood that a cancer patient will respondto cancer treatment regimen comprising a platinum and/or anthracycline.

Reference Values

In various embodiments of the present invention, the reference value isbased on BRCA1 gene expression in the cancer cell.

In various embodiments, the reference value for BLM expression or FANCIexpression is BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 10, 20,30, 40, 50, 60, 70, 80, or 90% compared to BRCA1 expression.

In various embodiments, the reference value is BRCA1 expression, and theBLM and/or FANCI expression is increased by at least or about 1-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold,1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold 2.3-fold 2.4-fold2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, or 3-fold, 4-fold,5-fold, 6-fold, 7-fold, 8-fold, 9-fold or 10-fold compared to BRCA1expression. In certain embodiments, the reference value is BRCA1expression, and the BLM and/or FANCI expression is increased by at leastor about two-fold to about 7-fold compared to BRCA1 expression.

In various embodiments of the present invention, the reference value canbe one or more housekeeping gene as described herein. In certainembodiments, one or more housekeeping gene as described herein, and theBLM and/or FANCI expression is increased by at least or about 10, 20,30, 40, 50, 60, 70, 80, or 90% compared to the one or more housekeepinggene expression.

In certain embodiments, one or more housekeeping gene as describedherein, and the BLM and/or FANCI expression is increased by at least orabout 1-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold,1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold 2.2-fold2.3-fold 2.4-fold 2.5-fold, 2.6-fold, 2.7-fold 2.8-fold 2.9-fold or3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold,20-fold, 30-fold, 40-fold, 50-fold, 60-fold or higher compared to theone or more housekeeping gene expression depending on the level of theexpression of the housekeeping gene in the cell.

In various embodiments, the housekeeping gene can be selected from thegroup consisting of beta-actin, GAPDH, RPLP0, GUS, TFRC and combinationsthereof. (See e.g., Cronin et al., Clinical Chemistry 53:6, 1084-1091(2007), and ONCOTYPE DX ASSAY®, herein incorporated by reference in itsentirety.) Thus, in some embodiments, the house keeping gene is one ofthese genes, and in other embodiments, the housekeeping gene is acombination of 2, 3, 4, or all 5 of these genes. In particularembodiments, the housekeeping gene is RPLP0, also called 36b4.

In various embodiments, the house keeping gene can be selected from thegenes listed in Table 1. Accordingly, in some embodiments, thehousekeeping gene is one of the genes from Table 1, and in otherembodiments, the housekeeping gene is a combination of any number or allof the genes from Table 1. (See e.g., Eisenberg and Levanon, Humanhousekeeping genes are compact. Trends in Genetics, Volume 19, Issue 7,362-365, 1 July 2003). Each gene name/description is followed by itsgeometric average expression level according to the data published by Suet al. Thus, based on our experimental data on the RPLP0 housekeepinggene as a reference gene, one of ordinary skill in the art can easilydetermine what the cut-off points for increased expression for any oneof these genes is. For example, genes designated by asterisk are inpopular use as reference in real-time PCR or quantitative PCR (qPCR),which is most often used in gene expression analysis.

In some aspects of all the embodiments on the invention, the assays,methods, kits, and systems incorporate qPCR as the gene expressionanalysis method to determine the amount compared to a reference value.

TABLE 1 Housekeeping Genes. Accession No. Description *NM_001101  Homosapiens actin, beta (ACTB), mRNA 6988 *NM_000034  Homo sapiens aldolaseA,fructose-bisphosphate (ALDOA), mRNA 3425 *NM_002046  Homo sapiensglyceraldehyde-3-phosphate dehydrogenase (GAPD), mRNA 828 *NM_000291 Homo sapiens phosphoglycerate kinase 1 (PGK1), mRNA 2727 *NM_005566 Homo sapiens lactate dehydrogenase A (LDHA), mRNA 2105 *NM_002954  Homosapiens ribosomal protein S27a (RPS27A), mRNA 4156 *NM_000981  Homosapiens ribosomal protein L19 (RPL19), mRNA 6997 *NM_000975  Homosapiens ribosomal protein L11 (RPL11), mRNA 6060 *NM_007363  Homosapiens non-POU domain containing, octamer- binding (NONO), mRNA 1708*NM_004309  Homo sapiens Rho GDP dissociation inhibitor (GDI) alpha(ARHGDIA), mRNA 1358 *NM_000994  Homo sapiens ribosomal protein L32(RPL32), mRNA 9523 *NM_022551  Homo sapiens ribosomal protein S18(RPS18), mRNA 11261 *NM_007355  Homo sapiens heat shock 90 kDa protein1, beta (HSPCB), mRNA 4119 NM_004515 Homo sapiens interleukin enhancerbinding factor 2, 45 kDa (ILF2), mRNA 1000 NM_004651 Homo sapiensubiquitin specific protease 11 (USP11), mRNA 1950 NM_004888 Homo sapiensATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G isoform 1(ATP6V1G1), mRNA 928 NM_003334 Homo sapiens ubiquitin-activating enzymeEl (A1S9T and BN75 temperature sensitivity complementing) (UBE1),transcript variant 1, mRNA 1351 NM_001320 Homo sapiens casein kinase 2,beta polypeptide (CSNK2B), mRNA 1233 NM_003915 Homo sapiens copine I(CPNE1), transcript variant 3, mRNA 698 NM_001250 Homo sapiens tumornecrosis factor receptor superfamily, member 5 (TNFRSF5), transcriptvariant 1, mRNA 524 NM_001904 Homo sapiens catenin (cadherin-associatedprotein), beta 1, 88 kDa (CTNNB1), mRNA 1165 NM_003753 Homo sapienseukaryotic translation initiation factor 3, subunit 7 zeta, 66/67 kDa(EIF3S7), mRNA 1363 NM_004541 Homo sapiens NADH dehydrogenase(ubiquinone) 1 alpha subcomplex, 1, 7.5 kDa (NDUFA1), nuclear geneencoding mitochondrial protein, mRNA 2307 NM_001654 Homo sapiens v-rafmurine sarcoma 3611 viral oncogene homolog 1 (ARAF1), mRNA 846 NM_002967Homo sapiens scaffold attachment factor B (SAFB), mRNA 545 NM_001183Homo sapiens ATPase, H+ transporting, lysosomal interacting protein 1(ATP6IP1), mRNA 1089 NM_003526 Homo sapiens H2B histone family, member L(H2BFL), mRNA 2232 NM_004718 Homo sapiens cytochrome c oxidase subunitVIIa polypeptide 2 like (COX7A2L), nuclear gene encoding mitochondrialprotein, mRNA 1013 NM_004436 Homo sapiens endosulfine alpha (ENSA), mRNA659 NM_001207 Homo sapiens basic transcription factor 3 (BTF3), mRNA3348 NM_004907 Homo sapiens immediate early protein (ETR101), mRNA 1249NM_004889 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0complex, subunit f, isoform 2 (ATP5J2), mRNA 1513 NM_003769 Homo sapienssplicing factor, arginine/serine-rich 9 (SFRS9), mRNA 1207 NM_003910Homo sapiens maternal G10 transcript (G10), mRNA 696 NM_000100 Homosapiens cystatin B (stefin B) (CSTB), mRNA 1422 NM_004785 Homo sapienssolute carrier family 9 (sodium/hydrogen exchanger), isoform 3regulatory factor 2 (SLC9A3R2), mRNA 455 NM_001120 Homo sapienstetracycline transporter-like protein (TETRAN), mRNA 935 NM_000182 Homosapiens hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme Athiolase/enoyl- Coenzyme A hydratase (trifunctional protein), alphasubunit (HADHA), mRNA 609 NM_003377 Homo sapiens vascular endothelialgrowth factor B (VEGFB), mRNA 649 NM_003576 Homo sapiensserine/threonine kinase 24 (STE20 homolog, yeast) (STK24), mRNA 769NM_000918 Homo sapiens procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfideisomerase; thyroid hormone binding protein p55) (P4HB), mRNA 2719NM_004584 Homo sapiens RAD9 homolog (S. pombe) (RAD9), mRNA 860NM_004952 Homo sapiens ephrin-A3 (EFNA3), mRNA 505 NM_004308 Homosapiens Rho GTPase activating protein 1 (ARHGAP1), mRNA 893 NM_003190Homo sapiens TAP binding protein (tapasin) (TAPBP), mRNA 1213 NM_004640Homo sapiens HLA-B associated transcript 1 (BAT1), transcript variant 1,mRNA 1022 NM_001064 Homo sapiens transketolase (Wernicke-Korsakoffsyndrome) (TKT), mRNA 1139 NM_002117 Homo sapiens majorhistocompatibility complex, class I, C (HLA-C), mRNA 4696 NM_004161 Homosapiens RAB1A, member RAS oncogene family (RAB1A), mRNA 2163 NM_003339Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)(UBE2D2), mRNA 514 NM_003969 Homo sapiens ubiquitin-conjugating enzymeE2M (UBC12 homolog, yeast) (UBE2M), mRNA 1197 NM_000516 Homo sapiensGNAS complex locus (GNAS), transcript variant 1, mRNA 4358 NM_002819Homo sapiens polypyrimidine tract binding protein 1 (PTBP1), transcriptvariant 1, mRNA 1138 NM_001001 Homo sapiens ribosomal protein L36a-like(RPL36AL), mRNA 1740 NM_004649 Homo sapiens chromosome 21 open readingframe 33 (C21orf33), mRNA 585 NM_000175 Homo sapiens glucose phosphateisomerase (GPI), mRNA 1633 NM_001867 Homo sapiens cytochrome c oxidasesubunit VIIc (COX7C), nuclear gene encoding mitochondrial protein, mRNA3004 NM_001967 Homo sapiens eukaryotic translation initiation factor 4A,isoform 2 (EIF4A2), mRNA 2935 NM_001863 Homo sapiens cytochrome coxidase subunit VIb (COX6B), nuclear gene encoding mitochondrialprotein, mRNA 1719 NM_001997 Homo sapiens Finkel-Biskis-Reilly murinesarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomalprotein S30 (FAU), mRNA 3898 NM_002088 Homo sapiens glutamate receptor,ionotropic, kainate 5 (GRIK5), mRNA 535 NM_001862 Homo sapienscytochrome c oxidase subunit Yb (COX5B), nuclear gene encodingmitochondrial protein, mRNA 1087 NM_004255 Homo sapiens cytochrome coxidase subunit Va (COX5A), nuclear gene encoding mitochondrial protein,mRNA 853 NM_001788 Homo sapiens CDC10 cell division cycle 10 homolog (S.cerevisiae) (CDC10), mRNA 1340 NM_004781 Homo sapiens vesicle-associatedmembrane protein 3 (cellubrevin) (VAMP3), mRNA 684 NM_003801 Homosapiens GPAA1P anchor attachment protein 1 homolog (yeast) (GPAA1), mRNA776 NM_004643 Homo sapiens poly(A) binding protein, nuclear 1 (PABPN1),mRNA 502 NM_001537 Homo sapiens heat shock factor binding protein 1(HSBP1), mRNA 874 NM_003680 Homo sapiens tyrosyl-tRNA synthetase (YARS),mRNA 535 NM_003345 Homo sapiens ubiquitin-conjugating enzyme E21 (UBC9homolog, yeast) (UBE2I), mRNA 1283 NM_002568 Homo sapiens poly(A)binding protein, cytoplasmic 1 (PABPC1), mRNA 3199 NM_001487 Homosapiens GCN5 general control of amino-acid synthesis 5-like 1 (yeast)(GCN5L1), mRNA 313 NM_001861 Homo sapiens cytochrome c oxidase subunitIV isoform 1 (COX4I1), nuclear gene encoding mitochondrial protein,mRNA2 738 NM_004890 Homo sapiens sperm associated antigen 7 (SPAG7),mRNA 618 NM_002812 Homo sapiens proteasome (prosome, macropain) 26Ssubunit, non-ATPase, 8 (PSMD8), mRNA 942 NM_004926 Homo sapiens zincfinger protein 36, C3H type-like 1 (ZFP36L1), mRNA 1168 NM_002539 Homosapiens ornithine decarboxylase 1 (ODC1), mRNA 1361 NM_000979 Homosapiens ribosomal protein L18 (RPL18), mRNA 4417 NM_000977 Homo sapiensribosomal protein L13 (RPL13), transcript variant 1, mRNA 6407 NM_001015Homo sapiens ribosomal protein S11 (RPS11), mRNA 7614 NM_001760 Homosapiens cyclin D3 (CCND3), mRNA 676 NM_003973 Homo sapiens ribosomalprotein L14 (RPL14), mRNA 3135 NM_002815 Homo sapiens proteasome(prosome, macropain) 26S subunit, non-ATPase, 11 (PSMD11), mRNA 536NM_000367 Homo sapiens thiopurine S-methyltransferase (TPMT), mRNA 1574NM_000973 Homo sapiens ribosomal protein L8 (RPL8), transcript variant1, mRNA 8138 NM_004689 Homo sapiens metastasis associated 1 (MTA1), mRNA506 NM_001848 Homo sapiens collagen, type VI, alpha 1 (COL6A1), mRNA 757NM_004068 Homo sapiens adaptor-related protein complex 2, mu 1 subunit(AP2M1), mRNA 2188 NM_001687 Homo sapiens ATP synthase, H+ transporting,mitochondrial F1 complex, delta subunit (ATP5D), mRNA 1167 NM_004197Homo sapiens serine/threonine kinase 19 (STK19), transcript variant 1,mRNA 574 NM_001028 Homo sapiens ribosomal protein S25 (RPS25), mRNA 4683NM_001022 Homo sapiens ribosomal protein S19 (RPS19), mRNA 6683NM_004759 Homo sapiens mitogen-activated protein kinase-activatedprotein kinase 2 (MAPKAPK2), transcript variant 1, mRNA 641 NM_001623Homo sapiens allograft inflammatory factor 1 (AIF1), transcript variant3, mRNA 497 NM_004894 Homo sapiens chromosome 14 open reading frame 2(C14orf2), mRNA 704 NM_002375 Homo sapiens microtubule-associatedprotein 4 (MAP4), transcript variant 1, mRNA 717 NM_001013 Homo sapiensribosomal protein S9 (RPS9), mRNA 6868 NM_003779 Homo sapiensUDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3(B4GALT3), mRNA 565 NM_001296 Homo sapiens chemokine binding protein 2(CCBP2), mRNA 394 NM_001009 Homo sapiens ribosomal protein S5 (RPS5),mRNA 6739 NM_003021 Homo sapiens small glutamine-rich tetratricopeptiderepeat (TPR)-containing (SGT), mRNA 488 NM_004285 Homo sapienshexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) (H6PD), mRNA646 NM_004142 Homo sapiens matrix metalloproteinase-like 1 (MMPL1), mRNA695 NM_001950 Homo sapiens E2F transcription factor 4, p107/p130-binding (E2F4), mRNA 956 NM_003815 Homo sapiens a disintegrin andmetalloproteinase domain 15 (metargidin) (ADAM15), mRNA 771 NM_001119Homo sapiens adducin 1 (alpha) (ADD1), transcript variant 1, mRNA 1356NM_001111 Homo sapiens adenosine deaminase, RNA-specific (ADAR),transcript variant ADAR-a, mRNA 1036 NM_003466 Homo sapiens paired boxgene 8 (PAX8), transcript variant PAX8A, mRNA 901 NM_001155 Homo sapiensannexin A6 (ANXA6), transcript variant 1, mRNA 718 NM_003465 Homosapiens chitinase 1 (chitotriosidase) (CHIT1), mRNA 561 NM_003186 Homosapiens transgelin (TAGLN), mRNA 1209 NM_000802 Homo sapiens folatereceptor 1 (adult) (FOLR1), transcript variant 2, mRNA 514 NM_004924Homo sapiens actinin, alpha 4 (ACTN4), mRNA 1187 NM_002931 Homo sapiensring finger protein 1 (RING 1), mRNA 576 NM_000020 Homo sapiens activinA receptor type II-like 1 (ACVRL1), mRNA 849 NM_001785 Homo sapienscytidine deaminase (CDA), mRNA 391 NM_004339 Homo sapiens pituitarytumor-transforming 1 interacting protein (PTTG1 IP), mRNA 1200 NM_003860Homo sapiens Breakpoint cluster region protein, uterine leiomyoma, 1;barrier to autointegration factor (BCRP1), mRNA 1303 NM_000214 Homosapiens jagged 1 (Alagille syndrome) (JAGO, mRNA 536 NM_002167 Homosapiens inhibitor of DNA binding 3, dominant negative helix-loop-helixprotein (ID3), mRNA 1192 NM_001664 Homo sapiens ras homolog gene family,member A (ARHA), mRNA 4050 NM_003166 Homo sapiens sulfotransferasefamily, cytosolic, 1A, phenol-preferring, member 3 (SULT1A3), mRNA 461NM_001746 Homo sapiens calnexin (CANX), mRNA 1923 NM_001662 Homo sapiensADP-ribosylation factor 5 (ARF5), mRNA 724 NM_001660 Homo sapiensADP-ribosylation factor 4 (ARF4), mRNA 1014 NM_001658 Homo sapiensADP-ribosylation factor 1 (ARF1), mRNA 2195 NM_003313 Homo sapienstissue specific transplantation antigen P35B (TSTA3), mRNA 440 NM_001494Homo sapiens GDP dissociation inhibitor 2 (GDI2), mRNA 1352 NM_003145Homo sapiens signal sequence receptor, beta (translocon- associatedprotein beta) (SSR2), mRNA 1265 NM_001619 Homo sapiens adrenergic, beta,receptor kinase 1 (ADRBK1), mRNA 695 NM_001420 Homo sapiens ELAV(embryonic lethal, abnormal vision, Drosophila)-like 3 (Hu antigen C)(ELAVL3), mRNA 1070 NM_004930 Homo sapiens capping protein (actinfilament) muscle Z- line, beta (CAPZB), mRNA 1183 NM_004596 Homo sapienssmall nuclear ribonucleoprotein polypeptide A (SNRPA), mRNA 734NM_004168 Homo sapiens succinate dehydrogenase complex, subunit A,flavoprotein (Fp) (SDHA), nuclear gene encoding mitochondrial protein,mRNA 1106 NM_004156 Homo sapiens protein phosphatase 2 (formerly 2A),catalytic subunit, beta isoform (PPP2CB), mRNA 1195 NM_004910 Homosapiens phosphatidylinositol transfer protein, membrane-associated(PITPNM), mRNA 869 NM_004517 Homo sapiens integrin-linked kinase (ILK),mRNA 654 NM_004494 Homo sapiens hepatoma-derived growth factor (high-mobility group protein 1-like) (HDGF), mRNA 1385 NM_004121 Homo sapiensgamma-glutamyltransferase-like activity 1 (GGTLA1), mRNA 412 NM_004404Homo sapiens neural precursor cell expressed, developmentallydown-regulated 5 (NEDD5), mRNA 1571 NM_004394 Homo sapiensdeath-associated protein (DAP), mRNA 623 NM_004383 Homo sapiens c-srctyrosine kinase (CSK), mRNA 899 NM_004074 Homo sapiens cytochrome coxidase subunit VIII (COX8), nuclear gene encoding mitochondrialprotein, mRNA 3188 NM_004039 Homo sapiens annexin A2 (ANXA2), mRNA 2417NM_001053 Homo sapiens somatostatin receptor 5 (SSTR5), mRNA 423NM_001328 Homo sapiens C-terminal binding protein 1 (CTBP1), mRNA 798NM_001273 Homo sapiens chromodomain helicase DNA binding protein 4(CHD4), mRNA 775 NM_003430 Homo sapiens zinc finger protein 91 (HPF7,HTF10) (ZNF91), mRNA 716 NM_003314 Homo sapiens tetratricopeptide repeatdomain 1 (TTC1), mRNA 651 NM_003217 Homo sapiens testis enhanced genetranscript (TEGT), mRNA 1766 NM_003132 Homo sapiens spermidine synthase(SRM), mRNA 1093 NM_000199 Homo sapiens N-sulfoglucosaminesulfohydrolase (sulfamidase) (SGSH), mRNA 565 NM_002818 Homo sapiensproteasome (prosome, macropain) activator subunit 2 (PA28 beta) (PSME2),mRNA 697 NM_002733 Homo sapiens protein kinase, AMP-activated, gamma 1non-catalytic subunit (PRKAG1), mRNA 497 NM_002631 Homo sapiensphosphogluconate dehydrogenase (PGD), mRNA 1009 NM_002574 Homo sapiensperoxiredoxin 1 (PRDX1), mRNA 2241 NM_002512 Homo sapiens non-metastaticcells 2, protein (NM23B) expressed in (NME2), nuclear gene encodingmitochondrial protein, mRNA 2553 NM_002455 Homo sapiens metaxin 1(MTX1), mRNA 845 NM_002444 Homo sapiens moesin (MSN), mRNA 1798NM_000529 Homo sapiens melanocortin 2 receptor (adrenocorticotropichormone) (MC2R), mRNA 420 NM_003573 Homo sapiens latent transforminggrowth factor beta binding protein 4 (LTBP4), mRNA 740 NM_002315 Homosapiens LIM_domain only 1 (rhombotin 1) (LMO1), mRNA 469 NM_000884 Homosapiens IMP (inosine monophosphate) dehydrogenase 2 (IMPDH2), mRNA 1288NM_003641 Homo sapiens interferon induced transmembrane protein 1 (9-27)(IFITM1), mRNA 4898 NM_000841 Homo sapiens glutamate receptor,metabotropic 4 (GRM4), mRNA 1369 NM_002070 Homo sapiens guaninenucleotide binding protein (G protein), alpha inhibiting activitypolypeptide 2 (GNAI2), mRNA 1877 NM_001493 Homo sapiens GDP dissociationinhibitor 1 (GDI1), mRNA 1387 NM_002048 Homo sapiens growtharrest-specific 1 (GAS1), mRNA 940 NM_002032 Homo sapiens ferritin,heavy polypeptide 1 (FTH1), mRNA 2616 NM_001418 Homo sapiens eukaryotictranslation initiation factor 4 gamma, 2 (EIF4G2), mRNA 3646 NM_001350Homo sapiens death-associated protein 6 (DAXX), mRNA 510 NM_001843 Homosapiens contactin 1 (CNTN1), mRNA 535 NM_001728 Homo sapiens basigin(BSG), mRNA 1508 NM_001667 Homo sapiens ADP-ribosylation factor-like 2(ARL2), mRNA 965 NM_001659 Homo sapiens ADP-ribosylation factor 3(ARF3), mRNA 1327 NM_003746 Homo sapiens dynein, cytoplasmic, lightpolypeptide 1 (DNCL1), mRNA 2758 NM_002127 Homo sapiens HLA-Ghistocompatibility antigen, class I, G (HLA-G), mRNA 1090 NM_004712 Homosapiens hepatocyte growth factor-regulated tyrosine kinase substrate(HGS), mRNA 505 NM_003475 Homo sapiens chromosome 11 open reading frame13 (C11orf13), mRNA 413 NM_004046 Homo sapiens ATP synthase, H+transporting, mitochondrial F1 complex, alpha subunit, isoform 1,cardiac muscle (ATP5A1), mRNA 1348 NM_001894 Homo sapiens casein kinase1, epsilon (CSNK1E), transcript variant 2, mRNA 613 NM_003795 Homosapiens sorting nexin 3 (SNX3), transcript variant 1, mRNA 1426NM_001909 Homo sapiens cathepsin D (lysosomal aspartyl protease) (CTSD),mRNA 1512 NM_002792 Homo sapiens proteasome (prosome, macropain)subunit, alpha type, 7 (PSMA7), transcript variant 1, mRNA 728 NM_002799Homo sapiens proteasome (prosome, macropain) subunit, beta type, 7(PSMB7), mRNA 545 NM_002300 Homo sapiens lactate dehydrogenase B (LDHB),mRNA 4144 NM_004176 Homo sapiens sterol regulatory element bindingtranscription factor 1 (SREBF1), mRNA 632 NM_002796 Homo sapiensproteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA 1229NM_002794 Homo sapiens proteasome (prosome, macropain) subunit, betatype, 2 (PSMB2), mRNA 1304 NM_002793 Homo sapiens proteasome (prosome,macropain) subunit, beta type, 1 (PSMB1), mRNA 2084 NM_002473 Homosapiens myosin, heavy polypeptide 9, non-muscle (MYH9), mRNA 1381NM_001810 Homo sapiens centromere protein B, 80 kDa (CENPB), mRNA 532NM_002624 Homo sapiens prefoldin 5 (PFDN5), transcript variant 1, mRNA1718 NM_004710 Homo sapiens synaptogyrin 2 (SYNGR2), mRNA 1414 NM_001127Homo sapiens adaptor-related protein complex 1, beta 1 subunit (AP1B1),transcript variant 1, mRNA 873 NM_002107 Homo sapiens H3 histone, family3A (H3F3A), mRNA 9328 NM_003899 Homo sapiens Rho guanine nucleotideexchange factor (GEF) 7 (ARHGEF7), transcript variant 1, mRNA 558NM_003406 Homo sapiens tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide (YWHAZ), transcriptvariant 1, mRNA 2008 NM_002419 Homo sapiens mitogen-activated proteinkinase kinase kinase 11 (MAP3K11), mRNA 535 NM_001130 Homo sapiensamino-terminal enhancer of split (AES), mRNA 2395 NM_003379 Homo sapiensvillin 2 (ezrin) (VIL2), mRNA 1356 NM_002636 Homo sapiens PHD fingerprotein 1 (PHF1), transcript variant 1, mRNA 640 NM_002622 Homo sapiensprefoldin 1 (PFDN1), mRNA 658 NM_001823 Homo sapiens creatine kinase,brain (CKB), mRNA 1407 NM_003405 Homo sapiens tyrosine3-monooxygenase/tryptophan 5- monooxygenase activation protein, etapolypeptide (YWHAH), mRNA 2195 NM_002939 Homo sapiensribonuclease/angiogenin inhibitor (RNH), mRNA 726 NM_003562 Homo sapienssolute carrier family 25 (mitochondrial carrier; oxoglutarate carrier),member 11 (SLC25A11), mRNA 517 NM_001916 Homo sapiens cytochrome c-1(CYC1), mRNA 895 NM_002823 Homo sapiens prothymosin, alpha (genesequence 28) (PTMA), mRNA 3723 NM_003096 Homo sapiens small nuclearribonucleoprotein polypeptide G (SNRPG), mRNA 687 NM_003321 Homo sapiensTu translation elongation factor, mitochondrial (TUFM), mRNA 1543NM_003404 Homo sapiens tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide (YWHAB), transcriptvariant 1, mRNA 1144 NM_002946 Homo sapiens replication protein A2, 32kDa (RPA2), mRNA 537 NM_004356 Homo sapiens CD81 antigen (target ofantiproliferative antibody 1) (CD81), mRNA 3638 NM_001743 Homo sapienscalmodulin 2 (phosphorylase kinase, delta) (CALM2), mRNA 4675 NM_004231Homo sapiens ATPase, H+ transporting, lysosomal 14 kDa, V1 subunit F(ATP6V1F), mRNA 997 NM_004893 Homo sapiens H2A histone family, member Y(H2AFY), transcript variant 2, mRNA 788 NM_004146 Homo sapiens NADHdehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18 kDa (NDUFB7), mRNA967 NM_002128 Homo sapiens high-mobility group box 1 (HMGB1), mRNA 1295NM_002002 Homo sapiens Fc fragment of IgE, low affinity II, receptor for(CD23A) (FCER2), mRNA 969 NM_000858 Homo sapiens guanylate kinase 1(GUK1), mRNA 1166 NM_001469 Homo sapiens thyroid autoantigen 70 kDa (Kuantigen) (G22P1), mRNA 1684 NM_003766 Homo sapiens beclin 1(coiled-coil, myosin-like BCL2 interacting protein) (BECN1), mRNA 948NM_003906 Homo sapiens MCM3 minichromosome maintenance deficient 3 (S.cerevisiae) associated protein (MCM3AP), mRNA 430 NM_000757 Homo sapienscolony stimulating factor 1 (macrophage) (CSF1), mRNA 797 NM_002149 Homosapiens hippocalcin-like 1 (HPCAL1), transcript variant 1, mRNA 1026NM_001694 Homo sapiens ATPase, H+ transporting, lysosomal 16 kDa, V0subunit c (ATP6V0C), mRNA 2105 NM_004047 Homo sapiens ATPase, H+transporting, lysosomal 21 kDa, V0 subunit c″ (ATP6V0B), mRNA 1212NM_001696 Homo sapiens ATPase, H+ transporting, lysosomal 31 kDa, V1subunit E isoform 1 (ATP6V1E1), mRNA 784 NM_001865 Homo sapienscytochrome c oxidase subunit VIIa polypeptide 2 (liver) (COX7A2),nuclear gene encoding mitochondrial protein, mRNA 1818 NM_004373 Homosapiens cytochrome c oxidase subunit VIa polypeptide 1 (COX6A1), nucleargene encoding mitochondrial protein, mRNA 5529 NM_000801 Homo sapiensFK506 binding protein 1A, 12 kDa (FKBP1A), transcript variant 12B, mRNA4273 NM_000992 Homo sapiens ribosomal protein L29 (RPL29), mRNA 6060NM_000988 Homo sapiens ribosomal protein L27 (RPL27), mRNA 6101NM_001004 Homo sapiens ribosomal protein, large P2 (RPLP2), mRNA 5924NM_001003 Homo sapiens ribosomal protein, large, P1 (RPLP1), mRNA 10300NM_000405 Homo sapiens GM2 ganglioside activator protein (GM2A), mRNA1250 NM_000967 Homo sapiens ribosomal protein L3 (RPL3), mRNA 7416NM_001428 Homo sapiens enolase 1, (alpha) (ENO1), mRNA 3668 NM_000999Homo sapiens ribosomal protein L38 (RPL38), mRNA 8302 NM_000997 Homosapiens ribosomal protein L37 (RPL37), mRNA 6689 NM_000995 Homo sapiensribosomal protein L34 (RPL34), transcript variant 1, mRNA 5424 NM_002948Homo sapiens ribosomal protein L15 (RPL15), mRNA 5450 NM_002952 Homosapiens ribosomal protein S2 (RPS2), mRNA 8825 NM_001026 Homo sapiensribosomal protein S24 (RP524), transcript variant 2, mRNA 5701 NM_001020Homo sapiens ribosomal protein S16 (RPS16), mRNA 7477 NM_001018 Homosapiens ribosomal protein S15 (RPS15), mRNA 6261 NM_001017 Homo sapiensribosomal protein S13 (RPS13), mRNA 5430 NM_000969 Homo sapiensribosomal protein L5 (RPL5), mRNA 4653 NM_000985 Homo sapiens ribosomalprotein L17 (RPL17), mRNA 4369 NM_000937 Homo sapiens polymerase (RNA)II (DNA directed) polypeptide A, 220 kDa (POLR2A), mRNA 753 NM_001016Homo sapiens ribosomal protein S12 (RPS12), mRNA 8265 NM_002140 Homosapiens heterogeneous nuclear ribonucleoprotein K (HNRPK), transcriptvariant 1, mRNA 2429 NM_002138 Homo sapiens heterogeneous nuclearribonucleoprotein D (AU-rich element RNA binding protein 1, 37 kDa)(HNRPD), transcript variant 3, mRNA 1157 NM_004499 Homo sapiensheterogeneous nuclear ribonucleoprotein A/B (HNRPAB), transcript variant2, mRNA 654 NM_001014 Homo sapiens ribosomal protein S10 (RPS10), mRNA8074 NM_002383 Homo sapiens MYC-associated zinc finger protein(purine-binding transcription factor) (MAZ), mRNA 2580 NM_002467 Homosapiens v-myc myelocytomatosis viral oncogene homolog (avian) (MYC),mRNA 537 NM_001436 Homo sapiens fibrillarin (FBL), mRNA 1408 NM_004069Homo sapiens adaptor-related protein complex 2, sigma 1 subunit (AP2S1),transcript variant AP17, mRNA 979 NM_001614 Homo sapiens actin, gamma 1(ACTG1), mRNA 6560 NM_002355 Homo sapiens mannose-6-phosphate receptor(cation dependent) (M6PR), mRNA 388 NM_004597 Homo sapiens small nuclearribonucleoprotein D2 polypeptide 16.5 kDa (SNRPD2), mRNA 1136 NM_002308Homo sapiens lectin, galactoside-binding, soluble, 9 (galectin 9)(LGALS9), transcript variant short, mRNA 888 NM_000398 Homo sapiensdiaphorase (NADH) (cytochrome b-5 reductase) (DIA1), nuclear geneencoding mitochondrial protein, transcript variant M, mRNA 2190NM_000754 Homo sapiens catechol-O-methyltransferase (COMT), transcriptvariant MB-COMT, mRNA 845 NM_002406 Homo sapiens mannosyl(alpha-1,3-)-glycoprotein beta- 1,2-N-acetylglucosaminyltransferase(MGAT1), mRNA 893 NM_003752 Homo sapiens eukaryotic translationinitiation factor 3, subunit 8, 110 kDa (EIF3S8), mRNA 1871 NM_001355Homo sapiens D-dopachrome tautomerase (DDT), mRNA 631 NM_004960 Homosapiens fusion, derived from t(12; 16) malignant liposarcoma (FUS), mRNA1019 NM_004729 Homo sapiens Ac-like transposable element (ALTE), mRNA963 NM_004587 Homo sapiens ribosome binding protein 1 homolog 180 kDa(dog) (RRBP1), mRNA 658 NM_004552 Homo sapiens NADH dehydrogenase(ubiquinone) Fe—S protein 5, 15 kDa (NADH-coenzyme Q reductase)(NDUFS5), mRNA 936 NM_004450 Homo sapiens enhancer of rudimentaryhomolog (Drosophila) (ERH), mRNA 1028 NM_004048 Homo sapiensbeta-2-microglobulin (B2M), mRNA 4992 NM_000239 Homo sapiens lysozyme(renal amyloidosis) (LYZ), mRNA 796 NM_000269 Homo sapiensnon-metastatic cells 1, protein (NM23A) expressed in (NME1), mRNA 887NM_000431 Homo sapiens mevalonate kinase (mevalonic aciduria) (MVK),mRNA 753 NM_001247 Homo sapiens ectonucleoside triphosphatediphosphohydrolase 6 (putative function) (ENTPD6), mRNA 495 NM_003365Homo sapiens ubiquinol-cytochrome c reductase core protein I (UQCRC1),mRNA 1026 NM_003329 Homo sapiens thioredoxin (TXN), mRNA 1002 NM_001069Homo sapiens tubulin, beta polypeptide (TUBB), mRNA 1013 NM_000356 Homosapiens Treacher Collins-Franceschetti syndrome 1 (TCOF1), mRNA 673NM_003134 Homo sapiens signal recognition particle 14 kDa (homologousAlu RNA binding protein) (SRP14), mRNA 2911 NM_003131 Homo sapiens serumresponse factor (c-fos serum response element-binding transcriptionfactor) (SRF), mRNA 664 NM_000454 Homo sapiens superoxide dismutase 1,soluble (amyotrophic lateral sclerosis 1 (adult)) (SOD1), mRNA 1739NM_003091 Homo sapiens small nuclear ribonucleoprotein polypeptides Band B1 (SNRPB), mRNA 1609 NM_003089 Homo sapiens small nuclearribonucleoprotein 70 kDa polypeptide (RNP antigen) (SNRP70), mRNA 1672NM_003016 Homo sapiens splicing factor, arginine/serine-rich 2 (SFRS2),mRNA 1476 NM_003952 Homo sapiens ribosomal protein S6 kinase, 70 kDa,polypeptide 2 (RPS6KB2), mRNA 476 NM_002950 Homo sapiens ribophorin I(RPN1), mRNA 495 NM_002743 Homo sapiens protein kinase C substrate 80K-H (PRKCSH), mRNA 691 NM_002686 Homo sapiens phenylethanolamineN-methyltransferase (PNMT), mRNA 501 NM_002654 Homo sapiens pyruvatekinase, muscle (PKM2), mRNA 2474 NM_002648 Homo sapiens pim-1 oncogene(PIM1), mRNA 1052 NM_002635 Homo sapiens solute carrier family 25(mitochondrial carrier; phosphate carrier), member 3 (SLC25A3), nucleargene encoding mitochondrial protein, transcript variant 1b, mRNA 2310NM_002494 Homo sapiens NADH dehydrogenase (ubiquinone) 1, subcomplexunknown, 1, 6 kDa (NDUFC1), mRNA 2247 NM_002488 Homo sapiens NADHdehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8 kDa (NDUFA2), mRNA689 NM_002434 Homo sapiens N-methylpurine-DNA glycosylase (MPG), mRNA1808 NM_002415 Homo sapiens macrophage migration inhibitory factor(glycosylation-inhibiting factor) (MIF), mRNA 3774 NM_002227 Homosapiens Janus kinase 1 (a protein tyrosine kinase) (JAK1), mRNA 990NM_001536 Homo sapiens HMT1 hnRNP methyltransferase-like 2 (S.cerevisiae) (HRMT1L2), mRNA 832 NM_000183 Homo sapienshydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme Athiolase/enoyl- Coenzyme A hydratase (trifunctional protein), betasubunit (HADHB), mRNA 1087 NM_002085 Homo sapiens glutathione peroxidase4 (phospholipid hydroperoxidase) (GPX4), mRNA 1279 NM_001502 Homosapiens glycoprotein 2 (zymogen granule membrane) (GP2), mRNA 572NM_002080 Homo sapiens glutamic-oxaloacetic transaminase 2,mitochondrial (aspartate aminotransferase 2) (GOT2), nuclear geneencoding mitochondrial protein, mRNA 1000 NM_001440 Homo sapiensexostoses (multiple)-like 3 (EXTL3), mRNA 592 NM_003754 Homo sapienseukaryotic translation initiation factor 3, subunit 5 epsilon, 47 kDa(EIF3S5), mRNA 1585 NM_003755 Homo sapiens eukaryotic translationinitiation factor 3, subunit 4 delta, 44 kDa (EIF3S4), mRNA 1085NM_003757 Homo sapiens eukaryotic translation initiation factor 3,subunit 2 beta, 36 kDa (EIF3S2), mRNA 622 NM_001360 Homo sapiens7-dehydrocholesterol reductase (DHCR7), mRNA 653 NM_001344 Homo sapiensdefender against cell death 1 (DAD1), mRNA 812 NM_001914 Homo sapienscytochrome b-5 (CYB5), nuclear gene encoding mitochondrial protein, mRNA667 NM_001834 Homo sapiens clathrin, light polypeptide (Lcb) (CLTB),transcript variant nonbrain, mRNA 447 NM_001833 Homo sapiens clathrin,light polypeptide (Lca) (CLTA), transcript variant nonbrain, mRNA 1315NM_001281 Homo sapiens cytoskeleton-associated protein 1 (CKAP1), mRNA1066 NM_001749 Homo sapiens calpain, small subunit 1 (CAPNS1), mRNA 1308NM_001697 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1complex, O subunit (oligomycin sensitivity conferring protein) (ATP5O),mRNA 1155 NM_001689 Homo sapiens ATP synthase, H+ transporting,mitochondrial F0 complex, subunit c (subunit 9) isoform 3 (ATP5G3), mRNA1152 NM_001675 Homo sapiens activating transcription factor 4 (tax-responsive enhancer element B67) (ATF4), mRNA 1392 NM_001642 Homosapiens amyloid beta (A4) precursor-like protein 2 (APLP2), mRNA 1341NM_014724 Homo sapiens zinc finger protein 305 (ZNF305), mRNA 719NM_005494 Homo sapiens DnaJ (Hsp40) homolog, subfamily B, member 6(DNAJB6), transcript variant 2, mRNA 923 NM_006597 Homo sapiens heatshock 70 kDa protein 8 (HSPA8), transcript variant 1, mRNA 1650NM_006623 Homo sapiens phosphoglycerate dehydrogenase (PHGDH), mRNA 888NM_015646 Homo sapiens RAP1B, member of RAS oncogene family (RAP1B),mRNA 736 NM_016532 Homo sapiens skeletal muscle and kidney enrichedinositol phosphatase (SKIP), transcript variant 1, mRNA 1529 NM_015292Homo sapiens likely ortholog of mouse membrane bound C2 domaincontaining protein (MBC2), mRNA 475 NM_005870 Homo sapienssin3-associated polypeptide, 18 kDa (SAP18), mRNA 1651 NM_006833 Homosapiens COP9 subunit 6 (MOV34 homolog, 34 kD) (COPS6), mRNA 1338NM_005718 Homo sapiens actin related protein 2/3 complex, subunit 4, 20kDa (ARPC4), mRNA 433 NM_005719 Homo sapiens actin related protein 2/3complex, subunit 3, 21 kDa (ARPC3), mRNA 949 NM_006372 Homo sapiensNS1-associated protein 1 (NSAP1), mRNA 704 NM_005180 Homo sapiens Blymphoma Mo-MLV insertion region (mouse) (BMI1), mRNA 732 NM_018975 Homosapiens telomeric repeat binding factor 2, interacting protein(TERF2IP), mRNA 684 NM_005731 Homo sapiens actin related protein 2/3complex, subunit 2, 34 kDa (ARPC2), transcript variant 2, mRNA 2262NM_020151 Homo sapiens START domain containing 7 (STARD7), transcriptvariant 1, mRNA 1562 NM_005103 Homo sapiens fasciculation and elongationprotein zeta 1 (zygin I) (FEZ1), transcript variant 1, mRNA 672NM_012179 Homo sapiens F-box only protein 7 (FBXO7), mRNA 865 NM_020360Homo sapiens phospholipid scramblase 3 (PLSCR3), mRNA 3645 NM_014891Homo sapiens PDGFA associated protein 1 (PDAP1), mRNA 1045 NM_005745Homo sapiens accessory protein BAP31 (DX51357E), mRNA 1525 NM_005418Homo sapiens suppression of tumorigenicity 5 (ST5), transcript variant1, mRNA 2305 NM_006262 Homo sapiens peripherin (PRPH), mRNA 484NM_133476 Homo sapiens zinc finger protein 384 (ZNF384), mRNA 448NM_006570 Homo sapiens Ras-related GTP-binding protein (RAGA), mRNA 903NM_006333 Homo sapiens nuclear DNA-binding protein (CID), mRNA 740NM_007285 Homo sapiens GABA(A) receptor-associated protein-like 2(GABARAPL2), mRNA 1265 NM_006354 Homo sapiens transcriptional adaptor3-like (TADA3L) transcript variant 1, mRNA 1060 NM_014302 Homo sapiensSec61 gamma (SEC61G), mRNA 644 NM_006118 Homo sapiens HS1 bindingprotein (HAX1), mRNA 1493 NM_012100 Homo sapiens aspartyl aminopeptidase(DNPEP), mRNA 419 NM_015680 Homo sapiens hypothetical protein CGI-57(CGI-57), mRNA 976 NM_030796 Homo sapiens hypothetical proteinDKFZp564K0822 (DKFZP564K0822), mRNA 572 NM_024069 Homo sapienshypothetical protein MGC2749 (MGC2749), mRNA 573 NM_013234 Homo sapiensmuscle specific gene (M9), mRNA 1056 NM_013310 Homo sapiens hypotheticalprotein AF038169 (AF038169), mRNA 1319 NM_018507 Homo sapienshypothetical protein PRO1843 (PRO1843), mRNA 1081 NM_017670 Homo sapienshypothetical protein FLJ20113 (FLJ20113), mRNA 999 NM_016292 Homosapiens heat shock protein 75 (TRAP1), mRNA 615 NM_014916 Homo sapiensKIAA1079 protein (KIAA1079), mRNA 772 NM_014696 Homo sapiens KIAA0514gene product (KIAA0514), mRNA 746 NM_014630 Homo sapiens KIAA0211 geneproduct (KIAA0211), mRNA 750 NM_014761 Homo sapiens KIAA0174 geneproduct (KIAA0174), mRNA 679 NM_007286 Homo sapiens synaptopodin(KIAA1029), mRNA 1349 NM_007263 Homo sapiens coatomer protein complex,subunit epsilon (COPE), mRNA 1272 NM_006349 Homo sapiens putative cyclinG1 interacting protein (CG1I), mRNA 591 NM_006004 Homo sapiensubiquinol-cytochrome c reductase hinge protein (UQCRH), mRNA 1285NM_005787 Homo sapiens Not56 (D. melanogaster)-like protein (NOT56L),mRNA 458 NM_012412 Homo sapiens histone H2A.F/Z variant (H2AV),transcript variant 1, mRNA 1070 NM_012401 Homo sapiens plexin B2(PLXNB2), mRNA 929 NM_007262 Homo sapiens RNA-binding protein regulatorysubunit (DJ-1), mRNA 1514 NM_007273 Homo sapiens repressor of estrogenreceptor activity (REA), mRNA 1804 NM_021009 Homo sapiens ubiquitin C(UBC), mRNA 8892 NM_023009 Homo sapiens macrophage myristoylatedalanine-rich C kinase substrate (MACMARCKS), mRNA 2025 NM_015456 Homosapiens cofactor of BRCA1 (COBRA1), mRNA 848 NM_005053 Homo sapiensRAD23 homolog A (S. cerevisiae) (RAD23A), mRNA 1015 NM_006830 Homosapiens ubiquinol-cytochrome c reductase (6.4 kD) subunit (UQCR), mRNA1489 NM_005682 Homo sapiens G protein-coupled receptor 56 (GPR56), mRNA742 NM_012102 Homo sapiens arginine-glutamic acid dipeptide (RE) repeats(RERE), mRNA 940 NM_005550 Homo sapiens kinesin family member C3(KIFC3), mRNA 603 NM_021960 Homo sapiens myeloid cell leukemia sequence1 (BCL2- related) (MCL1), mRNA 961 NM_021959 Homo sapiens proteinphosphatase 1, regulatory (inhibitor) subunit 11 (PPP1R11), mRNA 462NM_014730 Homo sapiens KIAA0152 gene product (KIAA0152), mRNA 713NM_014402 Homo sapiens low molecular mass ubiquinone-binding protein(9.5 kD) (QP-C), mRNA 2805 NM_007067 Homo sapiens histoneacetyltransferase (HBOA), mRNA 510 NM_006086 Homo sapiens tubulin, beta,4 (TUBB4), mRNA 2239 NM_014972 Homo sapiens KIAA1049 protein (KIAA1049),mRNA 1011 NM_024092 Homo sapiens hypothetical protein MGC5508 (MGC5508),mRNA 749 NM_021983 Homo sapiens major histocompatibility complex, classII, DR beta 4 (HLA-DRB4), mRNA 1095 NM_006510 Homo sapiens ret fingerprotein (RFP), transcript variant alpha, mRNA 420 NM_006711 Homo sapiensRNA binding protein Si, serine-rich domain (RNPS1), transcript variant1, mRNA 1376 NM_006145 Homo sapiens DnaJ (Hsp40) homolog, subfmaily B,member 1 (DNAJB1), mRNA 667 NM_033142 Homo sapiens chorionicgonadotropin, beta polypeptide 7 (CGB7), mRNA 773 NM_006351 Homo sapienstranslocase of inner mitochondrial membrane 44 homolog (yeast)(TIM1V144), mRNA 717 NM_014281 Homo sapiens fuse-bindingprotein-interacting repressor (SIABBP1), transcript variant 2, mRNA 632NM_012106 Homo sapiens binder of Arl Two (BART1), mRNA 760 NM_021975Homo sapiens v-rel reticuloendotheliosis viral oncogene homolog A,nuclear factor of kappa light polypeptide gene enhancer in B-cells 3,p65 (avian) (RELA), mRNA 767 NM_014874 Homo sapiens mitofusin 2 (MFN2),mRNA 453 NM_006796 Homo sapiens AFG3 ATPase family gene 3-like 2 (yeast)(AFG3L2), nuclear gene encoding mitochondrial protein, mRNA 724NM_006666 Homo sapiens RuvB-like 2 (E. coli) (RUVBL2), mRNA 690NM_005219 Homo sapiens diaphanous homolog 1 (Drosophila) (DIAPH1), mRNA592 NM_033546 Homo sapiens myosin regulatory light chain (MLC-B), mRNA1231 NM_032348 Homo sapiens hypothetical protein MGC3047 (MGC3047), mRNA553 NM_024798 Homo sapiens hypothetical protein FLJ13952 (FLJ13952),mRNA 2142 NM_021103 Homo sapiens thymosin, beta 10 (TMSB10), mRNA 1890NM_020195 Homo sapiens HCDI protein (HCDI), mRNA 612 NM_017432 Homosapiens prostate tumor over expressed gene 1 (PTOV1), mRNA 1509NM_014901 Homo sapiens KIAA1100 protein (KIAA1100), mRNA 1999 NM_014694Homo sapiens KIAA0605 gene product (KIAA0605), mRNA 532 NM_007369 Homosapiens G-protein coupled receptor (RE2), mRNA 963 NM_006156 Homosapiens neural precursor cell expressed, developmentally down-regulated8 (NEDD8), mRNA 867 NM_006429 Homo sapiens chaperonin containing TCP1,subunit 7 (eta) (CCT7), mRNA 1434 NM_006513 Homo sapiens seryl-tRNAsynthetase (SARS), mRNA 1130 NM_005022 Homo sapiens profilin 1 (PFN1),mRNA 2793 NM_014654 Homo sapiens syndecan 3 (N-syndecan) (SDC3), mRNA1082 NM_007209 Homo sapiens ribosomal protein L35 (RPL35), mRNA 3463NM_006082 Homo sapiens tubulin, alpha, ubiquitous (K-ALPHA-1), mRNA 4261NM_006362 Homo sapiens nuclear RNA export factor 1 (NXF1), mRNA 729NM_014228 Homo sapiens solute carrier family 6 (neurotransmittertransporter, L-proline), member 7 (SLC6A7), mRNA 1037 NM_006411 Homosapiens 1-acylglycerol-3-phosphate O- acyltransferase 1(lysophosphatidic acid acyltransferase, alpha) (AGPAT1), mRNA 742NM_021134 Homo sapiens mitochondrial ribosomal protein L23 (MRPL23),mRNA 771 NM_021974 Homo sapiens polymerase (RNA) II (DNA directed)polypeptide F (POLR2F), mRNA 1169 NM_006808 Homo sapiens proteintranslocation complex beta (SEC61B), mRNA 679 NM_005617 Homo sapiensribosomal protein S14 (RPS14), mRNA 7764 NM_005520 Homo sapiensheterogeneous nuclear ribonucleoprotein H1 (H) (HNRPH1), mRNA 2234NM_006755 Homo sapiens transaldolase 1 (TALDO1), mRNA 874 NM_006010 Homosapiens arginine-rich, mutated in early stage tumors (ARMET), mRNA 617NM_005088 Homo sapiens DNA segment on chromosome X and Y (unique) 155expressed sequence (DXYS155E), mRNA 524 NM_014754 Homo sapiensphosphatidylserine synthase 1 (PTDSS1), mRNA 930 NM_021953 Homo sapiensforkhead box M1 (FOXM1), mRNA 567 NM_006908 Homo sapiens ras-related C3botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)(RAC1), transcript variant Rac1, mRNA 1978 NM_014231 Homo sapiensvesicle-associated membrane protein 1 (synaptobrevin 1) (VAMP1),transcript variant VAMP- 1A, mRNA 745 NM_014833 Homo sapiens KIAA0618gene product (KIAA0618), mRNA 607 NM_005157 Homo sapiens v-abl Abelsonmurine leukemia viral oncogene homolog 1 (ABL1), transcript variant a,mRNA 777 NM_006325 Homo sapiens RAN, member RAS oncogene family (RAN),mRNA 3100 NM_007245 Homo sapiens ataxin 2 related protein (A2LP),transcript variant 1, mRNA 564 NM_007008 Homo sapiens reticulon 4(RTN4), mRNA 1267 NM_006782 Homo sapiens zinc finger protein-like 1(ZFPL1), mRNA 712 NM_006694 Homo sapiens jumping translocationbreakpoint (JTB), mRNA 2394 NM_006703 Homo sapiens nudix (nucleosidediphosphate linked moiety X)-type motif 3 (NUDT3), mRNA 566 NM_006032Homo sapiens copine VI (neuronal) (CPNE6), mRNA 1540 NM_012227 Homosapiens Pseudoautosomal GTP-binding protein- like (PGPL), mRNA 494NM_014604 Homo sapiens Tax interaction protein 1 (TIP-1), mRNA 748NM_021642 Homo sapiens Fc fragment of IgG, low affinity Ha, receptor for(CD32) (FCGR2A), mRNA 772 NM_005354 Homo sapiens jun D proto-oncogene(JUND), mRNA 4967 NM_020529 Homo sapiens nuclear factor of kappa lightpolypeptide gene enhancer in B-cells inhibitor, alpha (NFKBIA), mRNA 922NM_005561 Homo sapiens lysosomal-associated membrane protein 1 (LAMP1),mRNA 2865 NM_014774 Homo sapiens KIAA0494 gene product (KIAA0494), mRNA604 NM_014390 Homo sapiens EBNA-2 co-activator (100 kD) (p100), mRNA 867NM_014623 Homo sapiens male-enhanced antigen (MEA), mRNA 548 NM_014453Homo sapiens putative breast adenocarcinoma marker (32 kD) (BC-2), mRNA597 NM_012127 Homo sapiens Cip1-interacting zinc finger protein (CIZ1),mRNA 1051 NM_012099 Homo sapiens CD3-epsilon-associated protein;antisense to ERCC-1 (ASE-1), mRNA 472 NM_006888 Homo sapiens calmodulin1 (phosphorylase kinase, delta) (CALM1), mRNA 2161 NM_006867 Homosapiens RNA-binding protein gene with multiple splicing (RBPMS), mRNA1255 NM_006743 Homo sapiens RNA binding motif protein 3 (RBM3), mRNA2949 NM_006688 Homo sapiens C1q-related factor (CRF), mRNA 3604NM_006295 Homo sapiens valyl-tRNA synthetase 2 (VARS2), mRNA 721NM_006283 Homo sapiens transforming, acidic coiled-coil containingprotein 1 (TACC1), mRNA 867 NM_006221 Homo sapiens protein(peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1 (PIN1), mRNA561 NM_006148 Homo sapiens LIM_and SH3 protein 1 (LASP1), mRNA 1067NM_005954 Homo sapiens metallothionein 3 (growth inhibitory factor(neurotrophic)) (MT3), mRNA 2311 NM_006003 Homo sapiensubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1(UQCRFS1), nuclear gene encoding mitochondrial protein, mRNA 951NM_005998 Homo sapiens chaperonin containing TCP1, subunit 3 (gamma)(CCT3), mRNA 1098 NM_005997 Homo sapiens transcription factor-like 1(TCFL1), mRNA 505 NM_005629 Homo sapiens solute carrier family 6(neurotransmitter transporter, creatine), member 8 (SLC6A8), mRNA 628NM_005548 Homo sapiens lysyl-tRNA synthetase (KARS), mRNA 1193 NM_005545Homo sapiens immunoglobulin superfamily containing leucine-rich repeat(ISLR), mRNA 796 NM_005507 Homo sapiens cofilin 1 (non-muscle) (CFL1),mRNA 5155 NM_005381 Homo sapiens nucleolin (NCL), mRNA 2043 NM_005439Homo sapiens myeloid leukemia factor 2 (MLF2), mRNA 697 NM_006445 Homosapiens PRP8 pre-mRNA processing factor 8 homolog (yeast) (PRPF8), mRNA1384 NM_019059 Homo sapiens homolog of Tom7 (S. cerevisiae) (TOM7), mRNA2364 NM_006039 Homo sapiens mannose receptor, C type 2 (MRC2), mRNA 564NM_006066 Homo sapiens aldo-keto reductase family 1, member A1 (aldehydereductase) (AKR1A1), transcript variant 1, mRNA 879 NM_013318 Homosapiens hypothetical protein LQFBS-1 (LQFBS-1), mRNA 485 NM_006098 Homosapiens guanine nucleotide binding protein (G protein), beta polypeptide2-like 1 (GNB2L1), mRNA 7556 NM_007359 Homo sapiens M1LN51 protein(M1LN51), mRNA 975 NM_017510 Homo sapiens gp25L2 protein (HSGP25L2G),mRNA 1032 NM_015399 Homo sapiens breast cancer metastasis-suppressor 1(BRMS1), mRNA 476 NM_014508 Homo sapiens apolipoprotein B mRNA editingenzyme, catalytic polypeptide-like 3C (APOBEC3C), mRNA 816 NM_018955Homo sapiens ubiquitin B (UBB), mRNA 6074 NM_006368 Homo sapiens cAMPresponsive element binding protein 3 (luman) (CREB3), mRNA 533 NM_015024Homo sapiens RAN binding protein 16 (RANBP16), mRNA 559 NM_031420 Homosapiens mitochondrial ribosomal protein L9 (MRPL9), nuclear geneencoding mitochondrial protein, mRNA 476 NM_013232 Homo sapiensprogrammed cell death 6 (PDCD6), mRNA 816 NM_005917 Homo sapiens malatedehydrogenase 1, NAD (soluble) (MDH1), mRNA 1724 NM_032801 Homo sapiensjunctional adhesion molecule 3 (JAM3), mRNA 624 NM_030662 Homo sapiensmitogen-activated protein kinase kinase 2 (MAP2K2), mRNA 663 NM_006268Homo sapiens requiem, apoptosis response zinc finger gene (REQ), mRNA784 NM_006826 Homo sapiens tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide (YWHAQ), mRNA 1917NM_144582 Homo sapiens hypothetical protein MGC32043 (MGC32043), mRNA712 NM_144565 Homo sapiens hypothetical protein FLJ32334 (FLJ32334),mRNA 5319 NM_005984 Homo sapiens solute carrier family 25 (mitochondrialcarrier; citrate transporter), member 1 (SLC25A1), mRNA 620 NM_017828Homo sapiens hypothetical protein FLJ20452 (FLJ20452), mRNA 546NM_020150 Homo sapiens SARI protein (SARI), mRNA 581 NM_014610 Homosapiens alpha glucosidase II alpha subunit (G2AN), mRNA 1293 NM_014225Homo sapiens protein phosphatase 2 (formerly 2A), regulatory subunit A(PR 65), alpha isoform (PPP2R1A), mRNA 1687 NM_006937 Homo sapiens SMT3suppressor of mif two 3 homolog 2 (yeast) (SMT3H2), mRNA 2940 NM_005726Homo sapiens Ts translation elongation factor, mitochondrial (TSFM),mRNA 408 NM_005347 Homo sapiens heat shock 70 kDa protein 5 (glucose-regulated protein, 78 kDa) (HSPA5), mRNA 1111 NM_014255 Homo sapienstransmembrane protein 4 (TMEM4), mRNA 505 NM_006815 Homo sapiens coatedvesicle membrane protein (RNP24), mRNA 1642 NM_005456 Homo sapiensmitogen-activated protein kinase 8 interacting protein 1 (MAPK8IP1),mRNA 885 NM_005273 Homo sapiens guanine nucleotide binding protein (Gprotein), beta polypeptide 2 (GNB2), mRNA 1478 NM_007260 Homo sapienslysophospholipase II (LYPLA2), mRNA 2000 NM_007103 Homo sapiens NADHdehydrogenase (ubiquinone) flavoprotein 1, 51 kDa (NDUFV1), mRNA 803NM_017797 Homo sapiens BTB (POZ) domain containing 2 (BTBD2), mRNA 1030NM_016237 Homo sapiens anaphase promoting complex subunit 5 (ANAPC5),mRNA 935 NM_005801 Homo sapiens putative translation initiation factor(SUI1), mRNA 1058 NM_005216 Homo sapiensdolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST),mRNA 1421 NM_016457 Homo sapiens protein kinase D2 (PKD2), mRNA 662NM_006442 Homo sapiens DR1-associated protein 1 (negative cofactor 2alpha) (DRAP1), mRNA 561 NM_021019 Homo sapiens myosin, lightpolypeptide 6, alkali, smooth muscle and non-muscle (MYL6), transcriptvariant 1, mRNA 5933 NM_005112 Homo sapiens WD repeat domain 1 (WDR1),transcript variant 2, mRNA 809 NM_005370 Homo sapiens mel transformingoncogene (derived from cell line NK14)-RAB8 homolog (MEL), mRNA 682NM_006289 Homo sapiens talin 1 (TLN1), mRNA 1811 NM_005698 Homo sapienssecretory carrier membrane protein 3 (SCAMP3), transcript variant 1,mRNA 602 NM_ 024011 Homo sapiens cell division cycle 2-like 2 (CDC2L2),transcript variant 1, mRNA 430 NM_005105 Homo sapiens RNA binding motifprotein 8A (RBM8A), mRNA 785 NM_ 006013 Homo sapiens ribosomal proteinL10 (RPL10), mRNA 10721 NM_005786 Homo sapiens serologically definedcolon cancer antigen 33 (SDCCAG33), mRNA 1435 NM_007104 Homo sapiensribosomal protein L10a (RPL10A), mRNA 3006 NM_005762 Homo sapienstripartite motif-containing 28 (TRIM28), mRNA 1473 NM_012138 Homosapiens apoptosis antagonizing transcription factor (AATF), mRNA 504NM_015318 Homo sapiens Rho-specific guanine nucleotide exchange factorp114 (P114-RHO-GEF), mRNA 405 NM_012423 Homo sapiens ribosomal proteinL13a (RPL13A), mRNA 9545 NM_021128 Homo sapiens polymerase (RNA) II (DNAdirected) polypeptide L, 7.6 kDa (POLR2L), mRNA 1524 NM_032635 Homosapiens seven transmembrane domain protein (NIFIE14), mRNA 1121NM_005080 Homo sapiens X-box binding protein 1 (XBP1), mRNA 1772NM_006389 Homo sapiens hypoxia up-regulated 1 (HYOU1), mRNA 1076NM_024112 Homo sapiens chromosome 9 open reading frame 16 (C9orf16),mRNA 598 NM_006817 Homo sapiens chromosome 12 open reading frame 8(C12orf8), mRNA 910 NM_022830 Homo sapiens hypothetical protein FLJ22347(FLJ22347), mRNA 6021 NM_019884 Homo sapiens glycogen synthase kinase 3alpha (GSK3A), mRNA 963 NM_021107 Homo sapiens mitochondrial ribosomalprotein S12 (MRPS12), nuclear gene encoding mitochondrial protein,transcript variant 1, mRNA 828 NM_021074 Homo sapiens NADH dehydrogenase(ubiquinone) flavoprotein 2, 24 kDa (NDUFV2), mRNA 539 NM_014944 Homosapiens calsyntenin 1 (CLSTN1), mRNA 1620 NM_014764 Homo sapiens DAZassociated protein 2 (DAZAP2), mRNA 1802 NM_ 015343 Homo sapiens likelyortholog of Xenopus dullard (HSA011916), mRNA 933 NM_014420 Homo sapiensdickkopf homolog 4 (Xenopus laevis) (DKK4), mRNA 426 NM_005884 Homosapiens p21(CDKN1A)-activated kinase 4 (PAK4), mRNA 375 NM_012407 Homosapiens protein kinase C, alpha binding protein (PRKCABP), mRNA 553NM_012111 Homo sapiens chromosome 14 open reading frame 3 (C14orf3),mRNA 717 NM_007144 Homo sapiens zinc finger protein 144 (Mel-18)(ZNF144), mRNA 798 NM_007108 Homo sapiens transcription elongationfactor B (SIII), polypeptide 2 (18 kDa, elongin B) (TCEB2), mRNA 1192NM_007278 Homo sapiens GABA(A) receptor-associated protein (GABARAP),mRNA 2335 NM_007100 Homo sapiens ATP synthase, H+ transporting,mitochondrial F0 complex, subunit e (ATP5I), mRNA 2623 NM_006936 Homosapiens SMT3 suppressor of mif two 3 homolog 1 (yeast) (SMT3H1), mRNA1187 NM_006899 Homo sapiens isocitrate dehydrogenase 3 (NAD+) beta(IDH3B), mRNA 565 NM_006801 Homo sapiens KDEL (Lys-Asp-Glu-Leu) (SEQ IDNO: 1) endoplasmic reticulum protein retention receptor 1 (KDELR1), mRNA1270 NM_006612 Homo sapiens kinesin family member 1C (KIF1C), mRNA 600NM_006659 Homo sapiens tubulin, gamma complex associated protein 2(TUBGCP2), mRNA 701 NM_006595 Homo sapiens apoptosis inhibitor 5 (API5),mRNA 1173 NM_006401 Homo sapiens acidic (leucine-rich) nuclearphosphoprotein 32 family, member B (ANP32B), mRNA 2354 NM_006423 Homosapiens Rab acceptor 1 (prenylated) (RABAC1), mRNA 1706 NM_006460 Homosapiens HMBA-inducible (HIS1), mRNA 369 NM_006356 Homo sapiens ATPsynthase, H+ transporting, mitochondrial F0 complex, subunit d (ATP5H),mRNA 1047 NM_005891 Homo sapiens acetyl-Coenzyme A acetyltransferase 2(acetoacetyl Coenzyme A thiolase) (ACAT2), mRNA 911 NM_005839 Homosapiens serine/arginine repetitive matrix 1 (SRRM1), mRNA 745 NM_005594Homo sapiens nascent-polypeptide-associated complex alpha polypeptide(NACA), mRNA 3678 NM_005340 Homo sapiens histidine triad nucleotidebinding protein 1 (HINT1), mRNA 2270 NM_005175 Homo sapiens ATPsynthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit9), isoform 1 (ATP5G1), mRNA 1266 NM_005165 Homo sapiens aldolase C,fructose-bisphosphate (ALDOC), mRNA 1052 NM_005001 Homo sapiens NADHdehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5 kDa (NDUFA7),mRNA 806 NM_001402 NM_001958 NM_001961 NM_002714 NM_002808 NM_002809NM_004898 NM_007182 NM_032378

In various embodiments of the present invention, the reference value ischromosome 15 centromere copy number. In various embodiments, thereference value for chromosome 15q26 copy number is chromosome 15centromere copy number.

The chromosome 15q26 copy number and chromosome 15 centromere copynumber can be ascertained by various methods. For example, they can beascertained through chip based measurements with or without a normalreference, or by using centromeric FISH probes, which is an assay fortesting for copy number changes using microscopy.

In various embodiments, the number of chromosome 15 centromere probes iscompared to the number of 15q26.1 probes, in each cell using amicroscope. If the numbers match, there is no relative gain of 15q26.Increase in this context can be a numerical increase, e.g., 2-3 copies.In various embodiments, copy gain can be defined by the absolute copynumber determined in an interphase FISH assay averaged by counting aminimum of 20 tumor cells. In various embodiments, copy gain can bedefined as the ratio of 15q26/centromere 15 determined in an interphaseFISH assay counting both spots (15q26 and cent15) in the same cells andaveraging over a minimum of 20 cells. In various embodiments, copy gaincan be determined using a normalized genome wide assay such as SNParray, genome sequencing and the like, wherein the normalization is doneusing the ASCAT algorithm or other appropriate algorithms. In variousembodiments, the cutpoints can be anything above normal, which is 2absolute copies of 15q26, or ratio >1 for 15q26/cent15. Due to thetypical noise in these assays, in certain embodiments, the cutoff isdefined by adding a standard error. Accordingly, copy >2.6 or ratio >1.3signify copy number gain.

Thus, in various embodiments, a copy number gain of over 2.6 or a ratioof over 1.3 indicates a copy number gain in the sample.

In other embodiments, the reference value for chromosome 15q26 isdetermined from a non-cancer cell sample from the subject or a member ofthe same species to which the subject belongs. In certain embodiments,the reference value is determined from a non-cancerous cell or tissuesample that is the same type of cell or tissue as the cancer cell fromthe subject. In certain embodiments, the reference value is determinedfrom a non-cancerous cell or tissue sample that is not the same type ofcell or tissue as the cancer cell from the subject. In variousembodiments, array-based or sequencing-based technologies can be usedwherein the reference can be from patients' normal cells (e.g., blood),or it can be a collection of blood samples.

Copy number abnormalities can be detected using methods, such as, forexample, array CGH using BAC, cDNA and/or oligonucleotide arrays;microsatellite markers; STRs, RFLPS; etc.

Additional methods for evaluating copy number of nucleic acid in asample include, but are not limited to, hybridization-based assays. Onemethod for evaluating the copy number of encoding nucleic acid in asample involves a Southern Blot. In a Southern Blot, the genomic DNA(typically fragmented and separated on an electrophoretic gel) ishybridized to a probe specific for the target region. Comparison of theintensity of the hybridization signal from the probe for the targetregion with control probe signal from analysis of normal genomic DNA(e.g., a non-amplified portion of the same or related cell, tissue,organ, etc.) provides an estimate of the relative copy number of thetarget nucleic acid. Alternatively, a Northern blot may be utilized forevaluating the copy number of encoding nucleic acid in a sample. In aNorthern blot, mRNA is hybridized to a probe specific for the targetregion. Comparison of the intensity of the hybridization signal from theprobe for the target region with control probe signal from analysis ofnormal mRNA (e.g., a non-amplified portion of the same or related cell,tissue, organ, etc.) provides an estimate of the relative copy number ofthe target nucleic acid. Similar methods for determining copy number canbe performed using transcriptional arrays, which are well-known in theart.

An alternative means for determining the copy number is in situhybridization (e.g., Angerer (1987) Meth. Enzymol 152: 649). Generally,in situ hybridization comprises the following steps: (1) fixation oftissue or biological structure to be analyzed; (2) prehybridizationtreatment of the biological structure to increase accessibility oftarget DNA, and to reduce nonspecific binding; (3) hybridization of themixture of nucleic acids to the nucleic acid in the biological structureor tissue; (4) post-hybridization washes to remove nucleic acidfragments not bound in the hybridization and (5) detection of thehybridized nucleic acid fragments. The reagent used in each of thesesteps and the conditions for use vary depending on the particularapplication.

Preferred hybridization-based assays include, but are not limited to,traditional “direct probe” methods such as Southern blots or in situhybridization (e.g., FISH and FISH plus SKY), and “comparative probe”methods such as comparative genomic hybridization (CGH), e.g.,cDNA-based or oligonucleotide-based CGH. The methods can be used in awide variety of formats including, but not limited to, substrate (e.g.membrane or glass) bound methods or array-based approaches.

In a typical in situ hybridization assay, cells are fixed to a solidsupport, typically a glass slide. If a nucleic acid is to be probed, thecells are typically denatured with heat or alkali. The cells are thencontacted with a hybridization solution at a moderate temperature topermit annealing of labeled probes specific to the nucleic acid sequenceencoding the protein. The targets (e.g., cells) are then typicallywashed at a predetermined stringency or at an increasing stringencyuntil an appropriate signal to noise ratio is obtained.

The probes are typically labeled, e.g., with radioisotopes orfluorescent reporters. Preferred probes are sufficiently long so as tospecifically hybridize with the target nucleic acid(s) under stringentconditions. The preferred size range is from about 200 bases to about1000 bases.

In some applications it is necessary to block the hybridization capacityof repetitive sequences. Thus, in some embodiments, tRNA, human genomicDNA, or Cot-I DNA is used to block non-specific hybridization.

In CGH methods, a first collection of nucleic acids (e.g., from asample, e.g., a possible tumor) is labeled with a first label, while asecond collection of nucleic acids (e.g., a control, e.g., from ahealthy cell/tissue) is labeled with a second label. The ratio ofhybridization of the nucleic acids is determined by the ratio of the two(first and second) labels binding to each fiber in the array. Wherethere are chromosomal deletions or multiplications, differences in theratio of the signals from the two labels will be detected and the ratiowill provide a measure of the copy number. Array-based CGH may also beperformed with single-color labeling (as opposed to labeling the controland the possible tumor sample with two different dyes and mixing themprior to hybridization, which will yield a ratio due to competitivehybridization of probes on the arrays). In single color CGH, the controlis labeled and hybridized to one array and absolute signals are read,and the possible tumor sample is labeled and hybridized to a secondarray (with identical content) and absolute signals are read. Copynumber difference is calculated based on absolute signals from the twoarrays. Hybridization protocols suitable for use with the methods of theinvention are described, e.g., in Albertson (1984) EMBO J. 3: 1227-1234;Pinkel (1988) Proc. Natl. Acad. Sci. USA 85: 9138-9142; EPO Pub. No.430,402; Methods in Molecular Biology, Vol. 33: In situ HybridizationProtocols, Choo, ed., Humana Press, Totowa, N.J. (1994), etc. In oneembodiment, the hybridization protocol of Pinkel, et al. (1998) NatureGenetics 20: 207-211, or of Kallioniemi (1992) Proc. Natl Acad Sci USA89:5321-5325 (1992) is used.

The methods of the invention are particularly well suited to array-basedhybridization formats. Array-based CGH is described in U.S. Pat. No.6,455,258, the contents of which are incorporated herein by reference.In still another embodiment, amplification-based assays can be used tomeasure copy number. In such amplification-based assays, the nucleicacid sequences act as a template in an amplification reaction (e.g.,Polymerase Chain Reaction (PCR). In a quantitative amplification, theamount of amplification product will be proportional to the amount oftemplate in the original sample. Comparison to appropriate controls,e.g. healthy tissue, provides a measure of the copy number.

Methods of “quantitative” amplification are well known to those of skillin the art. For example, quantitative PCR involves simultaneouslyco-amplifying a known quantity of a control sequence using the sameprimers. This provides an internal standard that may be used tocalibrate the PCR reaction. Detailed protocols for quantitative PCR areprovided in Innis, et al. (1990) PCR Protocols, A Guide to Methods andApplications, Academic Press, Inc. N.Y.). Measurement of DNA copy numberat microsatellite loci using quantitative PCR anlaysis is described inGinzonger, et al. (2000) Cancer Research 60:5405-5409. The known nucleicacid sequence for the genes is sufficient to enable one of skill in theart to routinely select primers to amplify any portion of the gene.Fluorogenic quantitative PCR may also be used in the methods of theinvention. In fluorogenic quantitative PCR, quantitation is based onamount of fluorescence signals, e.g., TaqMan and sybr green.

Other suitable amplification methods include, but are not limited to,ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560,Landegren, et al. (1988) Science 241:1077, and Barringer et al. (1990)Gene 89: 117), transcription amplification (Kwoh, et al. (1989) Proc.Natl. Acad. Sci. USA 86: 1173), self-sustained sequence replication(Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874), dot PCR,and linker adapter PCR, etc.

In still other embodiments of the methods provided herein, sequencing ofindividual nucleic molecules (or their amplification products) isperformed, as an alternative to hybridization-based assays, usingnucleic acid sequencing techniques. In one embodiment, a high throughputparallel sequencing technique that isolates single nucleic acidmolecules of a population of nucleic acid molecules prior to sequencingmay be used. Such strategies may use so-called “next generationsequencing systems” including, without limitation, sequencing machinesand/or strategies well known in the art, such as those developed byIllumina/Solexa (the Genome Analyzer; Bennett et al. (2005)Pharmacogenomics, 6:373-20 382), by Applied Biosystems, Inc. (the SOLiDSequencer; solid.appliedbiosystems.com), by Roche (e.g., the 454 GS FLXsequencer; Margulies et al. (2005) Nature, 437:376-380; U.S. Pat. Nos.6,274,320; 6,258,568; 6,210,891), by Heliscope™ system from HelicosBiosciences (see, e.g., U.S. Patent App. Pub. No. 2007/0070349), and byothers. Other sequencing strategies such as stochastic sequencing (e.g.,as developed by Oxford Nanopore) may also be used, e.g., as described inInternational Application No. PCT/GB2009/001690 (pub. no.WO/2010/004273). All of the copy number determining strategies describedherein can similarly be applied to any of other nucleic acid-basedanalysis described herein, such as for BLM, FANCI, or 15q26 the likedescribed further below.

Therapies

These therapies can be selected, used, administered, etc., in accordancewith various embodiment of the present invention.

Platinum-comprising therapy, include but are not limited platinumchemotherapeutic agents, such as cisplatin, carboplatin, oxaliplatin,nedaplatin, and iproplatin. Other antineoplastic platinum coordinationcompounds are well known in the art, can be modified according towell-known methods in the art, and include the compounds disclosed inU.S. Pat. Nos. 4,996,337, 4,946,954, 5,091,521, 5,434,256, 5,527,905,and 5,633,243, all of which are incorporated herein by reference. Invarious embodiments described herein, the platinum comprising cancertherapy comprises cisplatinum or cis-diamminedichloroplatinum,phenanthriplatin, carboplatin, oxaliplatin, or a platinum complex thatis activated by ultraviolet A light.

In various embodiments, non-platinum comprising therapies include,non-platinum chemotherapy. Non-platinum chemotherapy may be, but is notlimited to, those selected from among the following groups of compounds:cytotoxic antibiotics, antimetabolities, anti-mitotic agents, alkylatingagents, arsenic compounds, DNA topoisomerase inhibitors, taxanes,nucleoside analogues, plant alkaloids, and toxins; and syntheticderivatives thereof. Exemplary compounds include, but are not limitedto, alkylating agents: treosulfan, and trofosfamide; plant alkaloids:vinblastine, paclitaxel, docetaxol; DNA topoisomerase inhibitors:doxorubicin, epirubicin, etoposide, camptothecin, topotecan, irinotecan,teniposide, crisnatol, and mitomycin; anti-folates: methotrexate,mycophenolic acid, and hydroxyurea; pyrimidine analogs: 5-fluorouracil,doxifluridine, and cytosine arabinoside; purine analogs: mercaptopurineand thioguanine; DNA antimetabolites: 2′-deoxy-5-fluorouridine,aphidicolin glycinate, and pyrazoloimidazole; and antimitotic agents:halichondrin, colchicine, and rhizoxin. Compositions comprising one ormore chemotherapeutic agents (e.g., FLAG, CHOP) may also be used. FLAGcomprises fludarabine, cytosine arabinoside (Ara-C) and G-CSF. CHOPcomprises cyclophosphamide, vincristine, doxorubicin, and prednisone. Inanother embodiments, PARP (e.g., PARP-1 and/or PARP-2) inhibitors areused and such inhibitors are well known in the art (e.g., Olaparib,ABT-888, BSI-201, BGP-15 (N-Gene Research Laboratories, Inc.); INO-1001(Inotek Pharmaceuticals Inc.); PJ34 (Soriano et al., 2001; Pacher etal., 2002b); 3-aminobenzamide (Trevigen); 4-amino-1,8-naphthalimide;(Trevigen); 6(5H)-phenanthridinone (Trevigen); benzamide (U.S. Pat. Re.36,397); and NU1025 (Bowman et al.). The foregoing examples ofnon-platinum chemotherapeutic agents are illustrative, and are notintended to be limiting.

In various embodiments, non-platinum comprising therapies include, forexample, radiation therapy. The radiation used in radiation therapy canbe ionizing radiation. Radiation therapy can also be gamma rays, X-rays,or proton beams. Examples of radiation therapy include, but are notlimited to, external-beam radiation therapy, interstitial implantationof radioisotopes (I-125, palladium, iridium), radioisotopes such asstrontium-89, thoracic radiation therapy, intraperitoneal P-32 radiationtherapy, and/or total abdominal and pelvic radiation therapy. For ageneral overview of radiation therapy, see Hellman, Chapter 16:Principles of Cancer Management: Radiation Therapy, 6th edition, 2001,DeVita et al., eds., J. B. Lippencott Company, Philadelphia. Theradiation therapy can be administered as external beam radiation orteletherapy wherein the radiation is directed from a remote source. Theradiation treatment can also be administered as internal therapy orbrachytherapy wherein a radioactive source is placed inside the bodyclose to cancer cells or a tumor mass. Also encompassed is the use ofphotodynamic therapy comprising the administration of photosensitizers,such as hematoporphyrin and its derivatives, Vertoporfin (BPD-MA),phthalocyanine, photosensitizer Pc4, demethoxy-hypocrellin A; and2BA-2-DMHA.

In various embodiments, non-platinum comprising therapies include, forexample, immunotherapy. Immunotherapy may comprise, for example, use ofcancer vaccines and/or sensitized antigen presenting cells. Theimmunotherapy can involve passive immunity for short-term protection ofa host, achieved by the administration of pre-formed antibody directedagainst a cancer antigen or disease antigen (e.g., administration of amonoclonal antibody, optionally linked to a chemotherapeutic agent ortoxin, to a tumor antigen). Immunotherapy can also focus on using thecytotoxic lymphocyte-recognized epitopes of cancer cell lines.

In various embodiments, non-platinum comprising therapies include, forexample, hormonal therapy, Hormonal therapeutic treatments can comprise,for example, hormonal agonists, hormonal antagonists (e.g., flutamide,bicalutamide, tamoxifen, raloxifene, leuprolide acetate (LUPRON), LH-RHantagonists), inhibitors of hormone biosynthesis and processing, andsteroids (e.g., dexamethasone, retinoids, deltoids, betamethasone,cortisol, cortisone, prednisone, dehydrotestosterone, glucocorticoids,mineralocorticoids, estrogen, testosterone, progestins), vitamin Aderivatives (e.g., all-trans retinoic acid (ATRA)); vitamin D3 analogs;antigestagens (e.g., mifepristone, onapristone), or antiandrogens (e.g.,cyproterone acetate).

In various embodiments described herein, the anthracycline isepirubincin or doxorubicin.

The duration and/or dose of treatment with anti-cancer therapies mayvary according to the particular anti-cancer agent or combinationthereof. An appropriate treatment time for a particular cancertherapeutic agent will be appreciated by the skilled artisan. Theinvention contemplates the continued assessment of optimal treatmentschedules for each cancer therapeutic agent, where the genetic signatureof the cancer of the subject as determined by the methods of theinvention is a factor in determining optimal treatment doses andschedules.

Cancers for which the Genetic Signature can be Determined

The methods of the invention can be used to determine the geneticsignature of many different cancers. Specific examples of types ofcancers for which the genetic signature can be determined by the methodsencompassed by the invention include, but are not limited to, humansarcomas and carcinomas, e.g., fibrosarcoma, myxosarcoma, liposarcoma,chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma,synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma,rhabdomyosarcoma, colon carcinoma, colorectal cancer, pancreatic cancer,breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma,basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceousgland carcinoma, papillary carcinoma, papillary adenocarcinomas,cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renalcell carcinoma, hepatoma, bile duct carcinoma, liver cancer,choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervicalcancer, bone cancer, brain tumor, testicular cancer, lung carcinoma,small cell lung carcinoma, bladder carcinoma, epithelial carcinoma,glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma,pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma,meningioma, melanoma, neuroblastoma, retinoblastoma; leukemias, e.g.,acute lymphocytic leukemia and acute myelocytic leukemia (myeloblastic,promyelocytic, myelomonocytic, monocytic and erythroleukemia); chronicleukemia (chronic myelocytic (granulocytic) leukemia and chroniclymphocytic leukemia); and polycythemia vera, lymphoma (Hodgkin'sdisease and non-Hodgkin's disease), multiple myeloma, Waldenstrom'smacroglobulinemia, and heavy chain disease.

In some embodiments, the cancer whose genetic signature is determined bythe method of the invention is an epithelial cancer such as, but notlimited to, bladder cancer, breast cancer, cervical cancer, coloncancer, gynecologic cancers, renal cancer, laryngeal cancer, lungcancer, oral cancer, head and neck cancer, ovarian cancer, pancreaticcancer, prostate cancer, or skin cancer. In other embodiments, thecancer is breast cancer, prostate cancer, lung cancer, or colon cancer.In still other embodiments, the epithelial cancer is non-small-cell lungcancer, nonpapillary renal cell carcinoma, cervical carcinoma, ovariancarcinoma (e.g., serous ovarian carcinoma), or breast carcinoma. Theepithelial cancers may be characterized in various other ways including,but not limited to, serous, endometrioid, mucinous, clear cell, brenner,or undifferentiated. In still other embodiments, the cancer is breastcancer, ovarian cancer or lung cancer. In particular embodiments, thecancer is triple negative breast cancer.

Subjects

In various embodiments, the subject for whom predicted efficacy of ananti-cancer therapy is determined, is a mammal (e.g., mouse, rat,primate, non-human mammal, domestic animal such as dog, cat, cow,horse), and is preferably a human. In another embodiment of the methodsof the invention, the subject has not undergone chemotherapy orradiation therapy. In alternative embodiments, the subject has undergonechemotherapy or radiation therapy (e.g., such as with cisplatin,carboplatin, and/or taxane). In related embodiments, the subject has notbeen exposed to levels of radiation or chemotoxic agents above thoseencountered generally or on average by the subjects of a species. Incertain embodiments, the subject has had surgery to remove cancerous orprecancerous tissue. In other embodiments, the cancerous tissue has notbeen removed, e.g., the cancerous tissue may be located in an inoperableregion of the body, such as in a tissue that is essential for life, orin a region where a surgical procedure would cause considerable risk ofharm to the patient, or e.g., the subject is given the anti-cancertherapy prior to removal of the cancerous tissue.

Nucleic Acid Sample Preparation

A. Nucleic Acid Isolation

Nucleic acid samples derived from cancerous and non-cancerous cells of asubject that can be used in the methods of the invention to determinethe genetic signature of a cancer can be prepared by means well known inthe art. For example, surgical procedures or needle biopsy aspirationcan be used to collect cancerous samples from a subject. In someembodiments, it is important to enrich and/or purify the canceroustissue and/or cell samples from the non-cancerous tissue and/or cellsamples. In other embodiments, the cancerous tissue and/or cell samplescan then be microdissected to reduce the amount of normal tissuecontamination prior to extraction of genomic nucleic acid or pre-RNA foruse in the methods of the invention. In still another embodiment, thecancerous tissue and/or cell samples are enriched for cancer cells by atleast 50%, 55%, 60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99%, or more or any range in between, in cancer cell content.Such enrichment can be accomplished according to methods well-known inthe art, such as needle microdissection, laser microdissection,fluorescence activated cell sorting, and immunological cell sorting. Inone embodiment, an automated machine performs the hyperproliferativecell enrichment to thereby transform the biological sample into apurified form enriched for the presence of hyperproliferative cells.

Collecting nucleic acid samples from non-cancerous cells of a subjectcan also be accomplished with surgery or aspiration. In surgicalprocedures where cancerous tissue is removed, surgeons often removenon-cancerous tissue and/or cell samples of the same tissue type of thecancer patient for comparison. Nucleic acid samples can be isolated fromsuch non-cancerous tissue of the subject for use in the methods of theinvention. In certain embodiments of the methods of the invention,nucleic acid samples from non-cancerous tissues are not derived from thesame tissue type as the cancerous tissue and/or cells sampled, and/orare not derived from the cancer patient. The nucleic acid samples fromnon-cancerous tissues may be derived from any non-cancerous and/ordisease-free tissue and/or cells. Such non-cancerous samples can becollected by surgical or non-surgical procedures. In certainembodiments, non-cancerous nucleic acid samples are derived fromtumor-free tissues. For example, non-cancerous samples may be collectedfrom lymph nodes, peripheral blood lymphocytes, and/or mononuclear bloodcells, or any subpopulation thereof. In a preferred embodiment, thenon-cancerous tissue is not pre-cancerous tissue, e.g., it does notexhibit any indicia of a pre-neoplastic condition such as hyperplasia,metaplasia, or dysplasia.

In one embodiment, the nucleic acid samples used to compute a referencevalue are taken from at least 1, 2, 5, 10, 20, 30, 40, 50, 100, or 200different organisms of that species. According to certain aspects of theinvention, nucleic acid “derived from” genomic DNA, as used in themethods of the invention, e.g., in hybridization experiments todetermine BLM expression, FANCI expression, or 15q26 copy number,chromosome 15 centromere copy number can be fragments of genomic nucleicacid generated by restriction enzyme digestion and/or ligation to othernucleic acid, and/or amplification products of genomic nucleic acids, orpre-messenger RNA (pre-mRNA), amplification products of pre-mRNA, orgenomic DNA fragments grown up in cloning vectors generated, e.g., by“shotgun” cloning methods. In certain embodiments, genomic nucleic acidsamples are digested with restriction enzymes.

B. Amplification of Nucleic Acids

Though the nucleic acid sample need not comprise amplified nucleic acid,in some embodiments, the isolated nucleic acids can be processed inmanners requiring and/or taking advantage of amplification. The genomicDNA samples of a subject optionally can be fragmented using restrictionendonucleases and/or amplified prior to determining analysis. In oneembodiment, the DNA fragments are amplified using polymerase chainreaction (PCR). Methods for practicing PCR are well known to those ofskill in the art. One advantage of PCR is that small quantities of DNAcan be used. For example, genomic DNA from a subject may be about 150ng, 175, ng, 200 ng, 225 ng, 250 ng, 275 ng, or 300 ng of DNA.

In certain embodiments of the methods of the invention, the nucleic acidfrom a subject is amplified using a single primer pair. For example,genomic DNA samples can be digested with restriction endonucleases togenerate fragments of genomic DNA that are then ligated to an adaptorDNA sequence which the primer pair recognizes. In other embodiments ofthe methods of the invention, the nucleic acid of a subject is amplifiedusing sets of primer pairs specific to BLM, FANCI, 15q26, or chromosome15 centromere copy and in instances wherein BRCA1, BRCA2, ER, PgR and/orHER2 receptor expression is also to be assessed, sets of primer pairsspecific to BRCA1, BRCA2, ER, PgR and/or HER2 receptor. Such sets ofprimer pairs each recognize genomic DNA sequences flanking BLM, FANCI,15q26, or chromosome 15 centromere and BRCA1, BRCA2, ER, PgR and/or HER2receptor wherein the expression is also to be assessed. A DNA samplesuitable for hybridization can be obtained, e.g., by polymerase chainreaction (PCR) amplification of genomic DNA, fragments of genomic DNA,fragments of genomic DNA ligated to adaptor sequences or clonedsequences. Computer programs that are well known in the art can be usedin the design of primers with the desired specificity and optimalamplification properties, such as Oligo version 5.0 (NationalBiosciences). PCR methods are well known in the art, and are described,for example, in Innis et al., eds., 1990, PCR Protocols: A Guide toMethods And Applications, Academic Press Inc., San Diego, Calif. It willbe apparent to one skilled in the art that controlled robotic systemsare useful for isolating and amplifying nucleic acids and can be used.

In other embodiments, where genomic DNA of a subject is fragmented usingrestriction endonucleases and amplified prior to analysis, theamplification can comprise cloning regions of genomic DNA of thesubject. In such methods, amplification of the DNA regions is achievedthrough the cloning process. For example, expression vectors can beengineered to express large quantities of particular fragments ofgenomic DNA of the subject (Sambrook, J. et al., eds., 1989, MolecularCloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., at pp. 9.47-9.51).

In yet other embodiments, where the DNA of a subject is fragmented usingrestriction endonucleases and amplified prior to analysis, theamplification comprises expressing a nucleic acid encoding a gene, or agene and flanking genomic regions of nucleic acids, from the subject.RNA (pre-messenger RNA) that comprises the entire transcript includingintrons is then isolated and used in the methods of the invention toanalyze and provide a genetic signature of a cancer. In certainembodiments, no amplification is required. In such embodiments, thegenomic DNA, or pre-RNA, of a subject may be fragmented usingrestriction endonucleases or other methods. The resulting fragments maybe hybridized to SNP probes. Typically, greater quantities of DNA areneeded to be isolated in comparison to the quantity of DNA or pre-mRNAneeded where fragments are amplified. For example, where the nucleicacid of a subject is not amplified, a DNA sample of a subject for use inhybridization may be about 400 ng, 500 ng, 600 ng, 700 ng, 800 ng, 900ng, or 1000 ng of DNA or greater. Alternatively, in other embodiments,methods are used that require very small amounts of nucleic acids foranalysis, such as less than 400 ng, 300 ng, 200 ng, 100 ng, 90 ng, 85ng, 80 ng, 75 ng, 70 ng, 65 ng, 60 ng, 55 ng, 50 ng, or less, such as isused for molecular inversion probe (MIP) assays. These techniques areparticularly useful for analyzing clinical samples, such as paraffinembedded formalin-fixed material or small core needle biopsies,characterized as being readily available but generally having reducedDNA quality (e.g., small, fragmented DNA) and/or not providing largeamounts of nucleic acids.

C. Hybridization

The nucleic acid samples derived from a subject used in the methods ofthe invention can be hybridized to arrays comprising probes (e.g.,oligonucleotide probes) in order to identify BLM, FANCI, 15q26, orchromosome 15 centromere and in instances wherein BRCA1, BRCA2, ER, PgRand/or HER2 receptor expression is also to be assessed, comprisingprobes in order to identify BRCA1, BRCA2, ER, PgR and/or HER2 receptor.Hybridization can also be used to determine whether the BLM, FANCI,15q26, or chromosome 15 centromere identified exhibit total copy numberchange, copy number gain, and copy number loss in nucleic acid samplesfrom cancerous tissues and/or cells of the subject. In preferredembodiments, the probes used in the methods of the invention comprise anarray of probes that can be tiled on a DNA chip (e.g., SNPoligonucleotide probes). In some embodiments, BLM expression, FANCIexpression, 15q26 copy number, or chromosome 15 centromere copy numberis determined by a method that does not comprise detecting a change insize of restriction enzyme-digested nucleic acid fragments. In otherembodiments, SNPs are analyzed to identify BLM expression or FANCIexpression, 15q26 copy number or chromosome 15 centromere copy number.Hybridization and wash conditions used in the methods of the inventionare chosen so that the nucleic acid samples to be analyzed by theinvention specifically bind or specifically hybridize to thecomplementary oligonucleotide sequences of the array, preferably to aspecific array site, wherein its complementary DNA is located. In someembodiments, the complementary DNA can be completely matched ormismatched to some degree as used, for example, in Affymetrixoligonucleotide arrays such as those used to analyze SNPs in MIP assays.The single-stranded synthetic oligodeoxyribonucleic acid DNA probes ofan array may need to be denatured prior to contact with the nucleic acidsamples from a subject, e.g., to remove hairpins or dimers which formdue to self-complementary sequences.

Optimal hybridization conditions will depend on the length of the probesand type of nucleic acid samples from a subject. General parameters forspecific (i.e., stringent) hybridization conditions for nucleic acidsare described in Sambrook, J. et al., eds., 1989, Molecular Cloning: ALaboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., at pp. 9.47-9.51 and 11.55-11.61; Ausubel et al.,eds., 1989, Current Protocols in Molecules Biology, Vol. 1, GreenPublishing Associates, Inc., John Wiley & Sons, Inc., New York, at pp.2.10.1-2.10.16. Exemplary useful hybridization conditions are providedin, e.g., Tijessen, 1993, Hybridization with Nucleic Acid Probes,Elsevier Science Publishers B. V. and Kricka, 1992, Nonisotopic DNAProbe Techniques, Academic Press, San Diego, Calif.

D. Oligonucleotide Nucleic Acid Arrays

In some embodiments of the methods of the present invention, DNA arrayscan be used to determine total copy number change, copy number gain, andcopy number loss by measuring the level of hybridization of the nucleicacid sequence to oligonucleotide probes that comprise complementarysequences. Hybridization can be used to determine the presence orabsence of heterozygosity. Various formats of DNA arrays that employoligonucleotide “probes,” (i.e., nucleic acid molecules having definedsequences) are well known to those of skill in the art. Typically, a setof nucleic acid probes, each of which has a defined sequence, isimmobilized on a solid support in such a manner that each differentprobe is immobilized to a predetermined region. In certain embodiments,the set of probes forms an array of positionally-addressable binding(e.g., hybridization) sites on a support. Each of such binding sitescomprises a plurality of oligonucleotide molecules of a probe bound tothe predetermined region on the support. More specifically, each probeof the array is preferably located at a known, predetermined position onthe solid support such that the identity (i.e., the sequence) of eachprobe can be determined from its position on the array (i.e., on thesupport or surface). Microarrays can be made in a number of ways, ofwhich several are described herein. However produced, microarrays sharecertain characteristics, they are reproducible, allowing multiple copiesof a given array to be produced and easily compared with each other.

Preferably, the microarrays are made from materials that are stableunder binding (e.g., nucleic acid hybridization) conditions. Themicroarrays are preferably small, e.g., between about 1 cm² and 25 cm²,preferably about 1 to 3 cm². However, both larger and smaller arrays arealso contemplated and may be preferable, e.g., for simultaneouslyevaluating a very large number of different probes. Oligonucleotideprobes can be synthesized directly on a support to form the array. Theprobes can be attached to a solid support or surface, which may be made,e.g., from glass, plastic (e.g., polypropylene, nylon), polyacrylamide,nitrocellulose, gel, or other porous or nonporous material. The set ofimmobilized probes or the array of immobilized probes is contacted witha sample containing labeled nucleic acid species so that nucleic acidshaving sequences complementary to an immobilized probe hybridize or bindto the probe. After separation of, e.g., by washing off, any unboundmaterial, the bound, labeled sequences are detected and measured. Themeasurement is typically conducted with computer assistance. Using DNAarray assays, complex mixtures of labeled nucleic acids, e.g., nucleicacid fragments derived a restriction digestion of genomic DNA fromnon-cancerous tissue, can be analyzed. DNA array technologies have madeit possible to determine the expression level or copy number BLM, FANCI,15q26, or chromosome 15 centromere, or BRCA1, BRCA2, ER, PgR and/or HER2receptor expression in instances where BRCA1, BRCA2, ER, PgR and/or HER2receptor expression is also assessed.

In certain embodiments, high-density oligonucleotide arrays are used inthe methods of the invention. These arrays containing thousands ofoligonucleotides complementary to defined sequences, at definedlocations on a surface can be synthesized in situ on the surface by, forexample, photolithographic techniques (see, e.g., Fodor et al., 1991,Science 251:767-773; Pease et al., 1994, Proc. Natl. Acad. Sci. U.S.A.91:5022-5026; Lockhart et al., 1996, Nature Biotechnology 14:1675; U.S.Pat. Nos. 5,578,832; 5,556,752; 5,510,270; 5,445,934; 5,744,305; and6,040,138). Methods for generating arrays using inkjet technology for insitu oligonucleotide synthesis are also known in the art (see, e.g.,Blanchard, International Patent Publication WO 98/41531, published Sep.24, 1998; Blanchard et al., 1996, Biosensors And Bioelectronics11:687-690; Blanchard, 1998, in Synthetic DNA Arrays in GeneticEngineering, Vol. 20, J. K. Setlow, Ed., Plenum Press, New York at pages111-123). Another method for attaching the nucleic acids to a surface isby printing on glass plates, as is described generally by Schena et al.(1995, Science 270:467-470). Other methods for making microarrays, e.g.,by masking (Maskos and Southern, 1992, Nucl. Acids. Res. 20:1679-1684),may also be used. When these methods are used, oligonucleotides (e.g.,15 to 60-mers) of known sequence are synthesized directly on a surfacesuch as a derivatized glass slide. The array produced can be redundant,with several oligonucleotide molecules corresponding to each informativelocus of interest (e.g., SNPs, RFLPs, STRs, etc.).

One exemplary means for generating the oligonucleotide probes of the DNAarray is by synthesis of synthetic polynucleotides or oligonucleotides,e.g., using N-phosphonate or phosphoramidite chemistries (Froehler etal., 1986, Nucleic Acid Res. 14:5399-5407; McBride et al., 1983,Tetrahedron Lett. 24:246-248). Synthetic sequences are typically betweenabout 15 and about 600 bases in length, more typically between about 20and about 100 bases, most preferably between about 40 and about 70 basesin length. In some embodiments, synthetic nucleic acids includenon-natural bases, such as, but by no means limited to, inosine. Asnoted above, nucleic acid analogues may be used as binding sites forhybridization. An example of a suitable nucleic acid analogue is peptidenucleic acid (see, e.g., Egholm et al., 1993, Nature 363:566-568; U.S.Pat. No. 5,539,083). In alternative embodiments, the hybridization sites(i.e., the probes) are made from plasmid or phage clones of regions ofgenomic DNA corresponding to SNPs or the complement thereof. The size ofthe oligonucleotide probes used in the methods of the invention can beat least 10, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length. It iswell known in the art that although hybridization is selective forcomplementary sequences, other sequences which are not perfectlycomplementary may also hybridize to a given probe at some level. Thus,multiple oligonucleotide probes with slight variations can be used, tooptimize hybridization of samples. To further optimize hybridization,hybridization stringency condition, e.g., the hybridization temperatureand the salt concentrations, may be altered by methods that are wellknown in the art.

In preferred embodiments, the high-density oligonucleotide arrays usedin the methods of the invention comprise oligonucleotides correspondingto BLM, FANCI, 15q26, or chromosome 15 centromere or in instanceswherein BRCA1, BRCA2, ER, PgR and/or HER2 receptor expression is alsoassessed, the arrays also comprise oligonucleotides corresponding toBRCA1, BRCA2, ER, PgR and/or HER2 receptor. The oligonucleotide probesmay comprise DNA or DNA “mimics” (e.g., derivatives and analogues)corresponding to a portion of each informative locus of interest (e.g.,SNPs, RFLPs, STRs, etc.) in a subject's genome. The oligonucleotideprobes can be modified at the base moiety, at the sugar moiety, or atthe phosphate backbone. Exemplary DNA mimics include, e.g.,phosphorothioates. For each SNP locus, a plurality of differentoligonucleotides may be used that are complementary to the sequences ofsample nucleic acids. For example, for a single informative locus ofinterest (e.g., SNPs, RFLPs, STRs, etc.) about 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, or more different oligonucleotides can be used. Eachof the oligonucleotides for a particular informative locus of interestmay have a slight variation in perfect matches, mismatches, and flankingsequence around the SNP. In certain embodiments, the probes aregenerated such that the probes for a particular informative locus ofinterest comprise overlapping and/or successive overlapping sequenceswhich span or are tiled across a genomic region containing the targetsite, where all the probes contain the target site. By way of example,overlapping probe sequences can be tiled at steps of a predeterminedbase interval, e. g. at steps of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 basesintervals. In certain embodiments, the assays can be performed usingarrays suitable for use with molecular inversion probe protocols such asdescribed by Wang et al. (2007) Genome Biol. 8, R246. Foroligonucleotide probes targeted at nucleic acid species of closelyresembled (i.e., homologous) sequences, “cross-hybridization” amongsimilar probes can significantly contaminate and confuse the results ofhybridization measurements. Cross-hybridization is a particularlysignificant concern in the detection of SNPs since the sequence to bedetected (i.e., the particular SNP) must be distinguished from othersequences that differ by only a single nucleotide. Cross-hybridizationcan be minimized by regulating either the hybridization stringencycondition and/or during post-hybridization washings. Highly stringentconditions allow detection of allelic variants of a nucleotide sequence,e.g., about 1 mismatch per 10-30 nucleotides. There is no singlehybridization or washing condition which is optimal for all differentnucleic acid sequences. For particular arrays of BLM, FANCI, 15q26, orchromosome 15 centromere, or of BRCA1, BRCA2, ER, PgR and/or HER2receptor these conditions can be identical to those suggested by themanufacturer or can be adjusted by one of skill in the art. In preferredembodiments, the probes used in the methods of the invention areimmobilized (i.e., tiled) on a glass slide called a chip. For example, aDNA microarray can comprises a chip on which oligonucleotides (purifiedsingle-stranded DNA sequences in solution) have been robotically printedin an (approximately) rectangular array with each spot on the arraycorresponds to a single DNA sample which encodes an oligonucleotide. Insummary the process comprises, flooding the DNA microarray chip with alabeled sample under conditions suitable for hybridization to occurbetween the slide sequences and the labeled sample, then the array iswashed and dried, and the array is scanned with a laser microscope todetect hybridization. In certain embodiments there are at least 250,500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000,10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000,19,000, 20,000, 21,000, 22,000, 23,000, 24,000, 25,000, 26,000, 27,000,28,000, 29,000, 30,000, 31,000, 32,000, 33,000, 34,000, 35,000, 36,000,37,000, 38,000, 39,000, 40,000, 41,000, 42,000, 43,000, 44,000, 45,000,50,000, 60,000, 70,000, 80,000, 90,000, 100,000 or more or any range inbetween, of BLM, FANCI, 15q26, or chromosome 15 centromere, or of BRCA1,BRCA2, ER, PgR and/or HER2 receptor for which probes appear on the array(with match/mismatch probes for a single locus of interest or probestiled across a single locus of interest counting as one locus ofinterest). The maximum number of BLM, FANCI, 15q26, or chromosome 15centromere, or of BRCA1, BRCA2, ER, PgR and/or HER2 receptor beingprobed per array is determined by the size of the genome and geneticdiversity of the subjects species. DNA chips are well known in the artand can be purchased in pre-5 fabricated form with sequences specific toparticular species. In some embodiments, the Genome-Wide Human SNP Array6.0™ and/or the 50K XbaI arrays (Affymetrix, Santa Clara, Calif.) areused in the methods of the invention. In other embodiments, SNPs and/orDNA copy number can be detected and quantitated using sequencingmethods, such as “next-generation sequencing methods” as describedfurther above.

E. Signal Detection

In some embodiments, nucleic acid samples derived from a subject arehybridized to the binding sites of an array described herein. In certainembodiments, nucleic acid samples derived from each of the two sampletypes of a subject (i.e., cancerous and non-cancerous) are hybridized toseparate, though identical, arrays. In certain embodiments, nucleic acidsamples derived from one of the two sample types of a subject (i.e.,cancerous and non-cancerous) is hybridized to such an array, thenfollowing signal detection the chip is washed to remove the firstlabeled sample and reused to hybridize the remaining sample. In otherembodiments, the array is not reused more than once. In certainembodiments, the nucleic acid samples derived from each of the twosample types of a subject (i.e., cancerous and non-cancerous) aredifferently labeled so that they can be distinguished. When the twosamples are mixed and hybridized to the same array, the relativeintensity of signal from each sample is determined for each site on thearray, and any relative difference in abundance of an allele of BLM,FANCI, 15q26, or chromosome 15 centromere, or of BRCA1, BRCA2, ER, PgRand/or HER2 receptor. Signals can be recorded and, in some embodiments,analyzed by computer. In one embodiment, the scanned image is despeckledusing a graphics program (e.g., Hij aak Graphics Suite) and thenanalyzed using an image gridding program that creates a spreadsheet ofthe average hybridization at each wavelength at each site. If necessary,an experimentally determined correction for “cross talk” (or overlap)between the channels for the two fluors may be made. For any particularhybridization site on the array, a ratio of the emission of the twofluorophores can be calculated, which may help in eliminating crosshybridization signals to more accurately determining whether aparticular SNP locus is heterozygous or homozygous.

F. Labeling

In some embodiments, the nucleic acids samples, fragments thereof, orfragments thereof ligated to adaptor regions used in the methods of theinvention are detectably labeled. For example, the detectable label canbe a fluorescent label, e.g., by incorporation of nucleotide analogues.Other labels suitable for use in the present invention include, but arenot limited to, biotin, iminobiotin, antigens, cofactors, dinitrophenol,lipoic acid, olefinic compounds, detectable polypeptides, electron richmolecules, enzymes capable of generating a detectable signal by actionupon a substrate, and radioactive isotopes.

Radioactive isotopes include that can be used in conjunction with themethods of the invention, but are not limited to, 32P and 14C.Fluorescent molecules suitable for the present invention include, butare not limited to, fluorescein and its derivatives, rhodamine and itsderivatives, texas red, 5′carboxy-fluorescein (“FAM”),2′,7′-dimethoxy-4′,5′-dichloro-6-carboxy-fluorescein (“JOE”), N, N,N′,N′-tetramethyl-6-carboxy-rhodamine (“TAMRA”), 6-carboxy-X-rhodamine(“ROX”), HEX, TET, IRD40, and IRD41.

Fluorescent molecules which are suitable for use according to theinvention further include: cyamine dyes, including but not limited toCy2, Cy3, Cy3.5, CY5, Cy5.5, Cy7 and FLUORX; BODIPY dyes including butnot limited to BODIPY-FL, BODIPY-TR, BODIPY-TMR, BODIPY-630/650, andBODIPY-650/670; and ALEXA dyes, including but not limited to ALEXA-488,ALEXA-532, ALEXA-546, ALEXA-568, and ALEXA-594; as well as otherfluorescent dyes which will be known to those who are skilled in theart. Electron rich indicator molecules suitable for the presentinvention include, but are not limited to, ferritin, hemocyanin, andcolloidal gold.

Two-color fluorescence labeling and detection schemes may also be used(Shena et al., 1995, Science 270:467-470). Use of two or more labels canbe useful in detecting variations due to minor differences inexperimental conditions (e.g., hybridization conditions). In someembodiments of the invention, at least 5, 10, 20, or 100 dyes ofdifferent colors can be used for labeling. Such labeling would alsopermit analysis of multiple samples simultaneously which is encompassedby the invention.

The labeled nucleic acid samples, fragments thereof, or fragmentsthereof ligated to adaptor regions that can be used in the methods ofthe invention are contacted to a plurality of oligonucleotide probesunder conditions that allow sample nucleic acids having sequencescomplementary to the probes to hybridize thereto. Depending on the typeof label used, the hybridization signals can be detected using methodswell known to those of skill in the art including, but not limited to,X-Ray film, phosphor imager, or CCD camera. When fluorescently labeledprobes are used, the fluorescence emissions at each site of a transcriptarray can be, preferably, detected by scanning confocal lasermicroscopy. In one embodiment, a separate scan, using the appropriateexcitation line, is carried out for each of the two fluorophores used.Alternatively, a laser can be used that allows simultaneous specimenillumination at wavelengths specific to the two fluorophores andemissions from the two fluorophores can be analyzed simultaneously (seeShalon et al. (1996) Genome Res. 6, 639-645). In a preferred embodiment,the arrays are scanned with a laser fluorescence scanner with a computercontrolled X-Y stage and a microscope objective. Sequential excitationof the two fluorophores is achieved with a multi-line, mixed gas laser,and the emitted light is split by wavelength and detected with twophotomultiplier tubes. Such fluorescence laser scanning devices aredescribed, e.g., in Schena et al. (1996) Genome Res. 6, 639-645.Alternatively, a fiber-optic bundle can be used such as that describedby Ferguson et al. (1996) Nat. Biotech. 14, 1681-1684. The resultingsignals can then be analyzed to determine the BLM expression, FANCIexpression, 15q26 copy number, or chromosome 15 centromere copy number,using computer software.

G. Algorithms for Analyzing BLM, FANCI, 15q26, or Chromosome 15Centromere

Once the hybridization signal has been detected the resulting data canbe analyzed using algorithms. In certain embodiments, the algorithm fordetermining the expression of BLM or FANCI, or copy number 15q26 orchromosome 15 centromere is based on well-known methods. Additionalrepresentative illustrations of such well known algorithms are providedin the Examples section below.

H. Computer Implementation Systems and Methods

In certain embodiments, the methods of the invention implement acomputer program to calculate a copy number, copy number gain, copynumber loss, and expression levels. For example, a computer program canbe used to perform the algorithms described herein. A computer systemcan also store and manipulate data generated by the methods of thepresent invention which comprises a plurality of hybridization signalchanges/profiles during approach to equilibrium in differenthybridization measurements and which can be used by a computer system inimplementing the methods of this invention. In certain embodiments, acomputer system receives probe hybridization data; (ii) stores probehybridization data; and (iii) compares probe hybridization data todetermine the state of BLM, FANCI, 15q26, or, chromosome 15 centromere,and/or of BRCA1, BRCA2, ER, PgR and/or HER2 receptor in said nucleicacid sample from cancerous or pre-cancerous tissue. The copy number,copy number gain, copy number loss, or expression levels is thencalculated. In some embodiments, a computer system (i) compares thedetermined copy number, copy number gain, copy number loss, andexpression levels to a threshold value or reference value; and (ii)outputs an indication of whether said copy number, copy number gain,copy number loss, and expression levels is above or below a thresholdvalue, or a genetic signature based on said indication. In certainembodiments, such computer systems are also considered part of thepresent invention.

Numerous types of computer systems can be used to implement the analyticmethods of this invention according to knowledge possessed by a skilledartisan in the bioinformatics and/or computer arts.

Several software components can be loaded into memory during operationof such a computer system. The software components can comprise bothsoftware components that are standard in the art and components that arespecial to the present invention (e.g., dCHIP software described in Linet al. (2004) Bioinformatics 20, 1233-1240; CRLMM software described inSilver et al. (2007) Cell 128, 991-1002; Aroma Affymetrix softwaredescribed in Richardson et al. (2006) Cancer Cell 9, 121-132. Themethods of the invention can also be programmed or modeled inmathematical software packages that allow symbolic entry of equationsand high-level specification of processing, including specificalgorithms to be used, thereby freeing a user of the need toprocedurally program individual equations and algorithms. Such packagesinclude, e.g., Matlab from Mathworks (Natick, Mass.), Mathematica fromWolfram Research (Champaign, Ill.) or S-Plus from MathSoft (Seattle,Wash.). In certain embodiments, the computer comprises a database forstorage of hybridization signal profiles. Such stored profiles can beaccessed and used to calculate a copy number, copy number gain, copynumber loss, or expression level. For example, of the hybridizationsignal profile of a sample derived from the non-cancerous tissue of asubject and/or profiles generated from population-based distributions ofBLM, FANCI, 15q26, or chromosome 15 centromere, and/or of BRCA1, BRCA2,ER, PgR and/or HER2 receptor in relevant populations of the same specieswere stored, it could then be compared to the hybridization signalprofile of a sample derived from the cancerous tissue of the subject.

In addition to the exemplary program structures and computer systemsdescribed herein, other, alternative program structures and computersystems will be readily apparent to the skilled artisan. Suchalternative systems, which do not depart from the above describedcomputer system and programs structures either in spirit or in scope,are therefore intended to be comprehended within the accompanyingclaims.

Once a laboratory technician or laboratory professional or group oflaboratory technicians or laboratory professionals determines whether asample has a copy number, copy number gain, copy number loss, orexpression level as described above (e.g., step (1) in many of themethods above), the same or a different laboratory technician orlaboratory professional (or group) can analyze a plurality of test BLM,FANCI, 15q26, or chromosome 15 centromere to determine whether there isa copy number, copy number gain, copy number loss, or expression level(e.g., step (2) in many of the methods above). Next, the same or adifferent laboratory technician or laboratory professional (or group)can combine the a copy number, copy number gain, copy number loss, orexpression level data from the test BLM, FANCI, 15q26, or chromosome 15centromere to derive a copy number, copy number gain, copy number loss,or expression level (e.g., step (3) in many of the methods above).Optionally, the same or a different laboratory technician or laboratoryprofessional (or group) can correlate the copy number, copy number gain,copy number loss, or expression level to an increased or decreasedlikelihood of response to a particular therapy (e.g., those mentionedabove).

In various embodiments, provided herein is a computer readable storagemedium comprising: a storing data module containing data from a samplecomprising a cancer cell obtained from a subject that represents anexpression level from an assay for BLM and/or FANCI, or copy number of15q26; a comparison module that compares the data stored on the storingdata module with a reference data and/or control data, and to provide acomparison content, and an output module displaying the comparisoncontent for the user, wherein the increased expression of BLM and/orFANCI, or copy number gain of 15q26 indicates that the subject issusceptible to platinum-comprising, or anthracycline-comprising cancertherapy.

In various embodiments, the control data comprises data from apopulation of non-cancerous healthy individuals. In various embodiments,the control data comprises data BRAC1 expression, and/or a housekeepinggene expression.

Embodiments of the invention can be described through functionalmodules, which are defined by computer executable instructions recordedon computer readable media and which cause a computer to perform methodsteps when executed. The modules are segregated by function, for thesake of clarity. However, it should be understood that themodules/systems need not correspond to discreet blocks of code and thedescribed functions can be carried out by the execution of various codeportions stored on various media and executed at various times.Furthermore, it should be appreciated that the modules may perform otherfunctions, thus the modules are not limited to having any particularfunctions or set of functions.

The computer readable storage media 30 can be any available tangiblemedia that can be accessed by a computer. Computer readable storagemedia includes volatile and nonvolatile, removable and non-removabletangible media implemented in any method or technology for storage ofinformation such as computer readable instructions, data structures,program modules or other data. Computer readable storage media includes,but is not limited to, RAM (random access memory), ROM (read onlymemory), EPROM (eraseable programmable read only memory), EEPROM(electrically eraseable programmable read only memory), flash memory orother memory technology, CD-ROM (compact disc read only memory), DVDs(digital versatile disks) or other optical storage media, magneticcassettes, magnetic tape, magnetic disk storage or other magneticstorage media, other types of volatile and non-volatile memory, and anyother tangible medium which can be used to store the desired informationand which can accessed by a computer including and any suitablecombination of the foregoing.

Computer-readable data embodied on one or more computer-readable mediamay define instructions, for example, as part of one or more programsthat, as a result of being executed by a computer, instruct the computerto perform one or more of the functions described herein, and/or variousembodiments, variations and combinations thereof. Such instructions maybe written in any of a plurality of programming languages, for example,Java, J#, Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic,COBOL assembly language, and the like, or any of a variety ofcombinations thereof. The computer-readable media on which suchinstructions are embodied may reside on one or more of the components ofeither of a system, or a computer readable storage medium describedherein, may be distributed across one or more of such components.

The computer-readable media may be transportable such that theinstructions stored thereon can be loaded onto any computer resource toimplement the aspects of the present invention discussed herein. Inaddition, it should be appreciated that the instructions stored on thecomputer-readable medium, described above, are not limited toinstructions embodied as part of an application program running on ahost computer. Rather, the instructions may be embodied as any type ofcomputer code (e.g., software or microcode) that can be employed toprogram a computer to implement aspects of the present invention. Thecomputer executable instructions may be written in a suitable computerlanguage or combination of several languages. Basic computationalbiology methods are known to those of ordinary skill in the art and aredescribed in, for example, Setubal and Meidanis et al., Introduction toComputational Biology Methods (PWS Publishing Company, Boston, 1997);Salzberg, Searles, Kasif, (Ed.), Computational Methods in MolecularBiology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler,Bioinformatics Basics: Application in Biological Science and Medicine(CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: APractical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc.,2nd ed., 2001).

The functional modules of certain embodiments of the invention; forexample, as depicted in FIG. 12, include for example, at a measuringmodule 40, a storage module 30, a comparison module 80, and an outputmodule 110. The functional modules can be executed on one, or multiple,computers, or by using one, or multiple, computer networks. Themeasuring module has computer executable instructions to provide e.g.,expression information in computer readable form.

The measuring module 40, can comprise any system for detecting theexpression of BLM and/or FANCI, the 15Q26 copy number. Such systems caninclude DNA microarrays, RNA expression arrays, any ELISA detectionsystem and/or any Western blotting detection system.

The information determined in the determination system can be read bythe storage module 30. As used herein the “storage module” is intendedto include any suitable computing or processing apparatus or otherdevice configured or adapted for storing data or information. Examplesof electronic apparatus suitable for use with the present inventioninclude stand-alone computing apparatus, data telecommunicationsnetworks, including local area networks (LAN), wide area networks (WAN),Internet, Intranet, and Extranet, and local and distributed computerprocessing systems. Storage modules also include, but are not limitedto: magnetic storage media, such as floppy discs, hard disc storagemedia, magnetic tape, optical storage media such as CD-ROM, DVD,electronic storage media such as RAM, ROM, EPROM, EEPROM and the like,general hard disks and hybrids of these categories such asmagnetic/optical storage media. The storage module is adapted orconfigured for having recorded thereon expression level or protein levelinformation. Such information may be provided in digital form that canbe transmitted and read electronically, e.g., via the Internet, ondiskette, via USB (universal serial bus) or via any other suitable modeof communication.

As used herein, “stored” refers to a process for encoding information onthe storage module. Those skilled in the art can readily adopt any ofthe presently known methods for recording information on known media togenerate manufactures comprising expression level information.

In one embodiment the reference data stored in the storage module to beread by the comparison module is e.g., expression data obtained from apopulation of non-cancer subjects, a population of cancer subjects orexpression data obtained from the same subject at a prior time pointusing the measuring module 40.

The “comparison module” 80 can use a variety of available softwareprograms and formats for the comparison operative to compare expressiondata determined in the measuring module to reference samples and/orstored reference data. In one embodiment, the comparison module isconfigured to use pattern recognition techniques to compare informationfrom one or more entries to one or more reference data patterns. Thecomparison module may be configured using existingcommercially-available or freely-available software for comparingpatterns, and may be optimized for particular data comparisons that areconducted. The comparison module provides computer readable informationrelated to normalized expression of BLM and/or FANCI, the 15Q26 copynumber in an individual, efficacy of treatment in an individual, and/ormethod for treating an individual.

The comparison module, or any other module of the invention, may includean operating system (e.g., UNIX) on which runs a relational databasemanagement system, a World Wide Web application, and a World Wide Webserver. World Wide Web application includes the executable codenecessary for generation of database language statements (e.g.,Structured Query Language (SQL) statements). Generally, the executableswill include embedded SQL statements. In addition, the World Wide Webapplication may include a configuration file which contains pointers andaddresses to the various software entities that comprise the server aswell as the various external and internal databases which must beaccessed to service user requests. The Configuration file also directsrequests for server resources to the appropriate hardware—as may benecessary should the server be distributed over two or more separatecomputers. In one embodiment, the World Wide Web server supports aTCP/IP protocol. Local networks such as this are sometimes referred toas “Intranets. An advantage of such Intranets is that they allow easycommunication with public domain databases residing on the World WideWeb (e.g., the GenBank or Swiss Pro World Wide Web site). Thus, in aparticular preferred embodiment of the present invention, users candirectly access data (via Hypertext links for example) residing onInternet databases using a HTML interface provided by Web browsers andWeb servers.

The comparison module provides a computer readable comparison resultthat can be processed in computer readable form by predefined criteria,or criteria defined by a user, to provide a content-based in part on thecomparison result that may be stored and output as requested by a userusing an output module 110.

The content based on the comparison result, may be an expression valuecompared to a reference showing the susceptibility or nonsusceptibilityof treatment with platinum-comprising therapy or anthracycline-comprising therapy.

In various embodiments of the invention, the content based on thecomparison result is displayed on a computer monitor 120. In variousembodiments of the invention, the content based on the comparison resultis displayed through printable media 130. The display module can be anysuitable device configured to receive from a computer and displaycomputer readable information to a user. Non-limiting examples include,for example, general-purpose computers such as those based on IntelPENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC,Hewlett-Packard PA-RISC processors, any of a variety of processorsavailable from Advanced Micro Devices (AMD) of Sunnyvale, Calif., or anyother type of processor, visual display devices such as flat paneldisplays, cathode ray tubes and the like, as well as computer printersof various types.

In one embodiment, a World Wide Web browser is used for providing a userinterface for display of the content based on the comparison result. Itshould be understood that other modules of the invention can be adaptedto have a web browser interface. Through the Web browser, a user mayconstruct requests for retrieving data from the comparison module. Thus,the user will typically point and click to user interface elements suchas buttons, pull down menus, scroll bars and the like conventionallyemployed in graphical user interfaces.

The present invention therefore provides for systems (and computerreadable media for causing computer systems) to perform methods forselecting treatment of cancer in an individual.

Systems and computer readable media described herein are merelyillustrative embodiments of the invention for detecting BLM and/or FANCIexpression, or 15Q26 copy number in an individual, and are not intendedto limit the scope of the invention. Variations of the systems andcomputer readable media described herein are possible and are intendedto fall within the scope of the invention.

The modules of the machine, or those used in the computer readablemedium, may assume numerous configurations. For example, function may beprovided on a single machine or distributed over multiple machines.

In some cases, a computing system provided herein can includecomputer-executable instructions or a computer program (e.g., software)containing computer-executable instructions for formatting an outputproviding an indication BLM and/or FANCI expression, 15q26 copy number,or a likelihood that a cancer patient will respond to a particularcancer treatment regimen (e.g., a regimen as described above), or acombination of these items. In some cases, a computing system providedherein can include computer-executable instructions or a computerprogram (e.g., software) containing computer-executable instructions fordetermining a desired cancer treatment regimen for a particular patientbased at least in part on increased expression of BLM and/or FANCI, or15q26 copy number gain.

In some cases, a computing system provided herein can include apre-processing device configured to process a sample (e.g., cancercells) such that a SNP array-based assay or sequencing-based assay canbe performed. Examples of pre-processing devices include, withoutlimitation, devices configured to enrich cell populations for cancercells as opposed to non-cancer cells, devices configured to lyse cellsand/or extract genomic nucleic acid, and devices configured to enrich asample for particular genomic DNA fragments.

The following numbered paragraphs provide some embodiments and aspectsof the invention.

-   -   1. An assay for selecting a therapy for a subject having cancer,        and optionally administering the therapy, the assay comprising:        -   subjecting a sample comprising a cancer cell taken from the            subject to an analysis for BLM and FANCI expression;        -   comparing the BLM and FANCI expression to a reference value;            and        -   selecting a platinum-comprising cancer therapy for the            subject when the BLM and FANCI expression is increased            compared to the reference value based on the recognition            that platinum-comprising cancer therapy is effective in            subjects whose cancer has increased expression of BLM and            FANCI, or selecting a non-platinum-comprising cancer therapy            for the subject when the BLM and FANCI expression is not            increased compared to the reference value based on the            recognition that platinum-comprising cancer therapy is not            effective in subjects whose cancer does not have increased            BLM and FANCI expression compared to the reference value.    -   2. The assay of paragraph 1, further comprising:        -   assaying the BRCA1 and/or BRCA2 status of the subject; and        -   selecting the platinum-comprising cancer therapy for the            subject when the subject is negative for BRCA1 and/or BRCA2            mutations, and the BLM and FANCI expression is increased            compared to the reference value based on the recognition            that platinum-comprising cancer therapy is effective in            subjects whose cancer has increased expression of BLM and            FANCI and who are negative for BRCA1 and/or BRCA2 mutations.    -   3. The assay of paragraph 1, the subject is known to be or is        determined to be negative for BRCA1 and/or BRCA2 mutations.    -   4. The assay of paragraph 1, further comprising:        -   assaying the estrogen receptor (ER), progesterone receptor            (PgR), and HER2 receptor status of the subject's cancer; and        -   selecting the platinum-comprising cancer therapy for the            subject when the subject's cancer does not express a            detectable quantity of ER, PgR, and HER2 receptor, and when            the BLM and FANCI expression is increased compared to the            reference value based on the recognition that            platinum-comprising cancer therapy is effective in subjects            whose cancer has increased expression of BLM and FANCI and            whose cancer does not express a detectable quantity of ER,            PgR, and HER2 receptor.    -   5. The assay of paragraph 1, wherein the subject's cancer or        cancer cell is known to not or is determined to not express a        detectable quantity of ER, PgR, and HER2 receptor.    -   6. The assay of paragraphs 1-5, further comprising administering        the selected therapy to the subject.    -   7. The assay of any one of the paragraphs 1-6, wherein the        cancer is selected from breast cancer, ovarian cancer and lung        cancer.    -   8. The assay of paragraphs 1-6, wherein the reference value is        BRCA1 expression in the sample and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   9. The assay of paragraphs 1-6, wherein the reference value is        based on at least BRCA1 gene expression in the cancer cell.    -   10. The assay paragraphs 1-6, wherein the reference value is        based on at least one housekeeping gene expression in the cancer        cell.    -   11. A method for selecting platinum-comprising therapy for a        subject having cancer, and optionally administering the        platinum-comprising therapy, the method comprising:        -   subjecting a sample comprising a cancer cell taken from the            subject to an analysis for BLM and FANCI expression;        -   detecting the BLM and FANCI expression in the sample            compared to a reference value; and        -   selecting a platinum-comprising cancer therapy for the            subject when the BLM and FANCI expression compared to a            reference value is increased based on the recognition that            platinum-comprising cancer therapy is effective in patients            whose cancer has increased BLM and FANCI expression compared            to the reference value.    -   12. The method of paragraph 11, further comprising administering        to the subject the platinum-comprising cancer therapy when the        platinum-comprising cancer therapy is selected.    -   13. The method of paragraph 11, wherein the subject is known to        be or is determined to be negative for BRCA1 and/or BRCA2        mutations.    -   14. The method of paragraph 11, wherein the subject's cancer or        cancer cell is known to not or determined to not express a        detectable quantity of ER, PgR, and HER2 receptor.    -   15. The method of any one of the paragraphs 11-14, wherein the        cancer is selected from breast cancer, ovarian cancer and lung        cancer.    -   16. The method of paragraph 11-15, wherein the reference value        is BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   17. The method of any one of the paragraphs 11-15, wherein the        reference value is based on at least BRCA1 gene expression in        the cancer cell.    -   18. The method of any one of the paragraphs 11-15, wherein the        reference value is based on at least one housekeeping gene        expression in the cancer cell.    -   19. The method of paragraph 18, wherein the housekeeping gene is        selected from beta-actin, GAPDH, RPLP0, GUS, TFRC and any        combination thereof.    -   20. The method of paragraph 19, wherein the housekeeping gene is        RPLP0, and the BLM and/or FANCI expression is increased by at        least six-fold.    -   21. A method for selecting a non-platinum-comprising therapy,        and optionally administering the non-platinum-comprising        therapy, for a subject having cancer comprising:        -   subjecting a sample comprising a cancer cell taken from the            subject to an analysis for BLM and FANCI expression;        -   detecting the BLM and FANCI expression in the sample            compared to a reference value; and        -   selecting the non-platinum-comprising cancer therapy for the            subject when the BLM and FANCI expression compared to the            reference value is not increased based on the recognition            that non-platinum-comprising cancer therapy is effective in            patients whose cancer does not have increased gene            expression of BLM and FANCI compared to the reference value.    -   22. The method of paragraph 21, further comprising administering        to the subject the non-platinum-comprising cancer therapy when        non-platinum-comprising cancer therapy is selected.    -   23. The method of any one of the paragraphs 21-22, wherein the        cancer is selected from breast cancer, ovarian cancer and lung        cancer.    -   24. The method of paragraph 21-23, wherein the reference value        is BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   25. The method of any one of the paragraphs 21-24, wherein the        reference value is based on at least BRCA1 gene expression in        the cancer cell.    -   26. The method of any one of the paragraphs 21-22, wherein the        reference value is based on at least one housekeeping gene        expression in the cancer cell.    -   27. An assay for selecting a therapy for a subject having        cancer, comprising:        -   subjecting a sample comprising a cancer cell taken from the            subject to an analysis for BLM and FANCI expression;        -   comparing the BLM and FANCI expression to a reference value;            and        -   selecting an anthracycline-compri sing cancer therapy for            the subject when the BLM and FANCI expression is increased            compared to a reference value based on the recognition that            anthracycline-comprising cancer therapy is effective in            subjects whose cancer has increased expression of BLM and            FANCI, or        -   selecting a non-anthracycline-comprising cancer therapy for            the subject when the BLM and FANCI expression is not            increased compared to a reference value based on the            recognition that anthracycline-comprising cancer therapy is            not effective in subjects whose cancer does not have            increased BLM expression compared to a reference value.    -   28. The assay of paragraph 27, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   29. A method for selecting an anthracycline-comprising cancer        therapy for a subject having cancer and determined to be        negative for BRCA1 and/or BRCA2 mutations, comprising:        -   subjecting a sample comprising a cancer cell taken from the            subject to an analysis for BLM and FANCI expression;        -   comparing the BLM and FANCI expression to a reference value;            and        -   selecting the anthracycline-comprising cancer therapy for            the subject when the BLM and FANCI expression compared to            the reference value is increased based on the recognition            that anthracycline-comprising cancer therapy is effective in            patients whose cancer has increased expression of BLM and            FANCI compared to the reference value.    -   30. The method of paragraph 29, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   31. A method of treating cancer in a human subject, comprising:        -   detecting BLM and FANCI expression in a sample comprising a            cancer cell taken from the human subject; and        -   comparing the BLM and FANCI expression to a reference value;            and        -   administering a platinum-comprising cancer therapy to the            human subject wherein an increase of BLM and FANCI            expression compared to the reference value is detected.    -   32. The method of paragraph 31, wherein the human subject's        cancer or cancer cell is known to not or is determined to not        express detectable quantities of estrogen receptor (ER),        progesterone receptor (PgR) and HER2 receptor.    -   33. The method of paragraph 31, wherein the cancer is selected        from breast, ovarian, and lung cancers.    -   34. The method of paragraph 31-33, wherein the reference value        is BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   35. The method of any one of the paragraphs 31-33, wherein the        reference value is based on BRCA1 gene expression in the cancer        cell.    -   36. The method of any one of the paragraphs 31-33, wherein the        reference value is based on a housekeeping gene expression in        the cancer cell.    -   37. A method of treating cancer in a human subject, comprising:        -   detecting BLM and FANCI expression in a sample comprising a            cancer cell taken from the human subject; and        -   comparing the BLM and FANCI expression to a reference value;            and        -   administering an anthracycline-comprising cancer therapy to            the human subject wherein an increase of BLM and FANCI            expression compared to the reference value is detected.    -   38. The method of paragraph 37, wherein the human subject's        cancer or cancer cell is known to not or is determined to not to        express detectable quantities of estrogen receptor (ER),        progesterone receptor (PgR) and HER2 receptor.    -   39. The method of paragraph 37, wherein the cancer is selected        from breast, ovarian, and lung cancers.    -   40. The method of paragraph 37-39, wherein the reference value        is BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   41. The method of any one of the paragraphs 37-39, wherein the        reference value is based on BRCA1 gene expression in the cancer        cell.    -   42. The method of any one of the paragraphs 37-39, wherein the        reference value is based on a housekeeping gene expression in        the cancer cell.    -   43. A method for assessing responsiveness of a cancer cell to        cancer therapy, comprising:        -   assaying, in a cancer cell or mRNA derived therefrom, BLM            and FANCI expression; and        -   comparing said BLM and FANCI expression to a reference            value, wherein the cancer cell is assessed as responsive to            a platinum-comprising therapy if the BLM and FANCI            expression is increased compared to the reference value, or            wherein the cancer cell is assessed as poorly or not            responsive to platinum-comprising cancer therapy cancer if            the BLM and FANCI expression is not increased.    -   44. The method of paragraph 43, wherein the step of assaying        comprises:        -   contacting the cancer cell or mRNA derived therefrom with at            least one detectably labeled probe capable of specifically            binding to BLM mRNA, at least one detectably probe capable            of specifically binding to FANCI, at least one detectably            labeled probe capable of specifically binding to BRCA1            and/or at least one housekeeping gene; and        -   measuring the expression of BLM and FANCI compared to the            BRCA1 and/or the at least one housekeeping gene.    -   45. The method of paragraph 43-44, wherein the reference value        is BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   46. A method of predicting a cancer patient's response to a        cancer treatment regimen comprising platinum or anthracycline,        comprising:        -   determining, in a cancer cell from the cancer patient, BLM            and FANCI expression; and        -   correlating the expression to a reference value, wherein            when the expression is increased the patient is predicted to            respond well to a cancer treatment regimen comprising            platinum or anthracycline.    -   47. The method of paragraph 46, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   48. A method of predicting a cancer patient's response to a        cancer treatment regimen comprising platinum or anthracycline,        comprising:        -   determining, in a cancer cell or mRNA derived therefrom from            said cancer patient, BLM and FANCI expression; and        -   correlating the expression to a reference value, wherein            when the expression is not increased the patient is            predicted to respond poorly to a cancer treatment regimen            comprising platinum or anthracycline.    -   49. The method of paragraph 48, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   50. A method of treating cancer, comprising:        -   assaying, in a cancer cell from a cancer patient or mRNA            obtained therefrom, the BLM and FANCI expression compared to            a reference value; and        -   administering to the cancer patient a cancer treatment            regimen comprising platinum or anthracycline if the BLM and            FANCI expression is increased compared to the reference            value.    -   51. The method of paragraph 50, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   52. Use of platinum comprising cancer therapy for treating a        cancer patient that has been determined to have a tumor        comprising cancer cells wherein BLM and FANCI expression is        increased compared to a reference value.    -   53. The use of paragraph 52, wherein the cancer patient has been        determined to be negative for BRCA1 and/or BRCA2 mutations.    -   54. The use of paragraph 52, wherein the cancer patient's cancer        or cancer cell is known to not or is determined to not express        detectable quantities of estrogen receptor (ER), progesterone        receptor (PgR) and HER2 receptor.    -   55. The use of paragraph 52-54, wherein the reference value is        BRCA1 expression in the sample, and the BLM and/or FANCI        expression is increased by at least two-fold compared to BRCA1        expression.    -   56. A system for determining responsiveness of a cancer cell to        platinum-comprising therapy from a cancer cell of a cancer        patient, comprising:        -   a sample analyzer configured to produce a signal for the            mRNA from each one of BLM and FANCI from a cancer cell            sample of a cancer patient; and        -   a computer sub-system programmed to calculate, based on the            mRNA whether the signal is greater or not than a reference            value.    -   57. The system of paragraph 56, wherein said computer sub-system        is programmed to compare the mRNA to determine        -   a likelihood of responsiveness of said cancer cell to            platinum-comprising cancer therapy based on an algorithm            that classifies the patient as likely to respond to a            platinum-comprising therapy if the BLM and FANCI expression            is increased and as unlikely to respond to the            platinum-comprising therapy if the BLM and FANCI expression            is not increased; or        -   a likelihood of responsiveness of said cancer cell to            anthracycline-comprising cancer therapy based on an            algorithm that classifies the patient as likely to respond            to a anthracycline-comprising therapy if the BLM and FANCI            expression is increased and as unlikely to respond to the            anthracycline-comprising therapy if the BLM and FANCI            expression is not increased.    -   58. The system of paragraph 56-57, wherein the reference value        is BRCA1 expression, and the BLM and/or FANCI expression is        increased by at least two-fold compared to BRCA1 expression.    -   59. A computer program product embodied in a computer readable        medium that, when executing on a computer, performs steps        comprising:        -   detecting the BLM and FANCI gene expression in sample            comprising a cancer cell from a cancer patient; and        -   comparing the BLM and FANCI expression to a reference value.    -   60. The computer program of paragraph 59, wherein the reference        value is BRCA1 expression, and the BLM and/or FANCI expression        is increased by at least two-fold compared to BRCA1 expression.    -   61. A diagnostic kit for detecting a likelihood of a cancer        patient to respond to platinum- or anthracycline-comprising        comprising cancer therapy, comprising:        -   no more than 10 probes comprising a combination of            detectably labeled probes or primers for BLM and FANCI, and            optionally for BRCA1 and/or at least one housekeeping gene;            and        -   the computer program product of Paragraph 59.    -   62. Use of a plurality of oligonucleotides comprising no more        than 10 oligonucleotides capable of hybridizing to BLM and        FANCI, and optionally to BRCA1 and/or at least one housekeeping        gene, in a diagnostic kit for determining an increased        likelihood that a cancer patient will respond to cancer        treatment regimen comprising a platinum and/or anthracycline.    -   63. The use, method or assay of any one of the preceding        paragraphs, wherein said anthracycline is epirubincin or        doxorubicin.    -   64. The use, method or assay of any one of the preceding        paragraphs, wherein said platinum comprising cancer therapy        comprises cisplatinum or cis-diamminedichloroplatinum,        phenanthriplatin, carboplatin, oxaliplatin, or a platinum        complex that is activated by ultraviolet A light.    -   65. An assay for selecting a therapy for a subject having        cancer, and optionally administering the therapy, the assay        comprising:        -   assaying a sample comprising a cancer cell taken from the            subject for a chromosome 15q26 copy number;        -   comparing the chromosome 15q26 copy number to a reference            value; and        -   selecting a platinum-comprising cancer therapy for the            subject if there is a chromosome 15q26 copy number gain            compared to the reference value, or selecting a            non-platinum-comprising cancer therapy for the subject if            there is not a chromosome 15q26 copy number gain, or if            there is a chromosome 15q26 copy number loss.    -   66. The assay of paragraph 65, further comprising:        -   assaying the BRCA1 and/or BRCA2 status of the subject; and        -   selecting the platinum-comprising cancer therapy for the            subject when the subject is negative for BRCA1 and/or BRCA2            mutations, and there is a chromosome 15q26 copy number gain            based on the recognition that platinum-comprising cancer            therapy is effective in subjects who have a chromosome 15q26            copy number gain who are negative for BRCA1 and/or BRCA2            mutations.    -   67. The assay of paragraph 65, the subject is known to be or is        determined to be negative for BRCA1 and/or BRCA2 mutations.    -   68. The assay of paragraph 65, further comprising:        -   assaying the estrogen receptor (ER), progesterone receptor            (PgR), and HER2 receptor status of the subject's cancer; and        -   selecting the platinum-comprising cancer therapy for the            subject when the subject's cancer does not express a            detectable quantity of ER, PgR, and HER2 receptor, and when            there is a chromosome 15q26 copy number gain based on the            recognition that platinum-comprising cancer therapy is            effective in subjects who have a chromosome 15q26 copy            number gain and whose cancer does not express a detectable            quantity of ER, PgR, and HER2 receptor.    -   69. The assay of paragraph 65, wherein the subject's cancer or        cancer cell is known to not or is determined to not express a        detectable quantity of ER, PgR, and HER2 receptor.    -   70. The assay of paragraphs 65-69, further comprising        administering the selected therapy to the subject.    -   71. The assay of paragraphs 65-71, wherein the cancer is        selected from breast cancer, ovarian cancer and lung cancer.    -   72. The assay of paragraphs 65-71, wherein the reference value        is chromosome 15 centromere copy number in the sample.    -   73. An assay for selecting a therapy for a subject having        cancer, and optionally administering the therapy, the assay        comprising:        -   assaying a sample comprising a cancer cell taken from the            subject for a chromosome 15q26 copy number;        -   comparing the chromosome 15q26 copy number to a reference            value; and        -   selecting an anthracycline-comprising cancer therapy for the            subject if there is a chromosome 15q26 copy number gain            compared to the reference value, or selecting a            non-anthracycline-comprising cancer therapy for the subject            if there is not a chromosome 15q26 copy number gain, or if            there is a chromosome 15q26 copy number loss.    -   74. The assay of paragraph 73, further comprising:        -   assaying the BRCA1 and/or BRCA2 status of the subject; and        -   selecting the anthracycline-comprising cancer therapy for            the subject when the subject is negative for BRCA1 and/or            BRCA2 mutations, and there is a chromosome 15q26 copy number            gain based on the recognition that anthracycline-comprising            cancer therapy is effective in subjects who have a            chromosome 15q26 copy number gain who are negative for BRCA1            and/or BRCA2 mutations.    -   75. The assay of paragraph 73, the subject is known to be or is        determined to be negative for BRCA1 and/or BRCA2 mutations.    -   76. The assay of paragraph 73, further comprising:        -   assaying the estrogen receptor (ER), progesterone receptor            (PgR), and HER2 receptor status of the subject's cancer; and        -   selecting the anthracycline-comprising cancer therapy for            the subject when the subject's cancer does not express a            detectable quantity of ER, PgR, and HER2 receptor, and when            there is a chromosome 15q26 copy number gain based on the            recognition that anthracycline-comprising cancer therapy is            effective in subjects who have a chromosome 15q26 copy            number gain and whose cancer does not express a detectable            quantity of ER, PgR, and HER2 receptor.    -   77. The assay of paragraph 73, wherein the subject's cancer or        cancer cell is known to not or is determined to not express a        detectable quantity of ER, PgR, and HER2 receptor.    -   78. The assay of paragraphs 73-77, further comprising        administering the selected therapy to the subject.    -   79. The assay of paragraphs 73-78, wherein the cancer is        selected from breast cancer, ovarian cancer and lung cancer.    -   80. The assay of paragraphs 73-79, wherein the reference value        is chromosome 15 centromere copy number in the sample.    -   81. A method of treating cancer in a human subject, comprising:        -   detecting a chromosome 15q26 copy number in a sample            comprising a cancer cell taken from the subject;        -   comparing the chromosome 15q26 copy number to a reference            value; and        -   administering an platinum-comprising cancer therapy for the            subject if there is a chromosome 15q26 copy number gain            compared to the reference value, or administering a            non-platinum-comprising cancer therapy for the subject if            there is not a chromosome 15q26 copy number gain, or if            there is a chromosome 15q26 copy number loss.    -   82. The method of paragraphs 81, wherein the cancer is selected        from breast cancer, ovarian cancer and lung cancer.    -   83. The method of paragraphs 81-82, wherein the reference value        is chromosome 15 centromere copy number in the sample.    -   84. The method of paragraph 81-83, wherein the subject's cancer        is known to not express a detectable quantity of ER, PgR, and        HER2 receptor.    -   85. A method of treating cancer in a human subject, comprising:        -   detecting a chromosome 15q26 copy number in a sample            comprising a cancer cell taken from the subject;        -   comparing the chromosome 15q26 copy number to a reference            value; and        -   administering an anthracycline-comprising cancer therapy for            the subject if there is a chromosome 15q26 copy number gain            compared to the reference value, or administering a            non-anthracycline-comprising cancer therapy for the subject            if there is not a chromosome 15q26 copy number gain, or if            there is a chromosome 15q26 copy number loss.    -   86. The method of paragraphs 85, wherein the cancer is selected        from breast cancer, ovarian cancer and lung cancer.    -   87. The method of paragraphs 85-86, wherein the reference value        is chromosome 15 centromere copy number in the sample.    -   88. The method of paragraph 85-88, wherein the subject's cancer        or cancer cell is known to not or is determined to not express a        detectable quantity of ER, PgR, and HER2 receptor.    -   89. A method for assessing responsiveness of a cancer cell to a        cancer therapy, and optionally administering the cancer therapy,        comprising:        -   assaying a sample comprising a cancer cell taken from the            subject for a chromosome 15q26 copy number;        -   and comparing the chromosome 15q26 copy number to a            reference value, wherein the cancer cell is assessed as            responsive to a platinum-comprising therapy if there is a            chromosome 15q26 copy number gain compared to the reference            value, or wherein the cancer cell is assessed as poorly or            not responsive to platinum-comprising cancer therapy cancer            if there is not a chromosome 15q26 copy number gain or if            there is a chromosome 15q26 copy number loss.    -   90. The method of paragraph 89, wherein the reference value is        copy number of chromosome 15. 91. The method of paragraph 89,        wherein the cancer is selected from breast cancer, ovarian        cancer and lung cancer.    -   92. The method of paragraph 89, further comprising administering        the platinum-comprising therapy if there is a chromosome 15q26        copy number gain.    -   93. A method of predicting a cancer patient's response to a        cancer treatment regimen comprising platinum or anthracycline,        comprising:        -   determining, in a cancer cell from the cancer patient,            chromosome 15q26 copy number; and        -   correlating the chromosome 15q26 copy number to a reference            value,        -   wherein when there is a chromosome 15q26 copy number gain,            the patient is predicted to respond well to a cancer            treatment comprising platinum or anthracycline, or wherein            when there is not a chromosome 15q26 copy number gain or a            chromosome 15q26 copy number loss, the patient is predicted            respond poorly to a cancer treatment comprising platinum or            anthracycline.    -   94. The method of paragraph 93, wherein the reference value is        chromosome 15 centromere copy number in the sample.    -   95. Use of platinum comprising cancer therapy for treating a        cancer patient that has been determined to have a tumor        comprising cancer cells wherein a chromosome 15q26 copy gain is        detected compared to a reference value.    -   96. The use of paragraph 95, wherein the cancer patient is known        to be or is determined to be negative for BRCA1 and/or BRCA2        mutations.    -   97. The use of paragraph 95, wherein the cancer patient's cancer        or cancer cell is known to not or is determined to not express        detectable quantities of estrogen receptor (ER), progesterone        receptor (PgR) and HER2 receptor.    -   98. The use of paragraph 95-97, wherein the reference value is        chromosome 15 centromere copy number in the sample.    -   99. A system for determining responsiveness of a cancer cell to        platinum-comprising therapy from a cancer cell of a cancer        patient, comprising:        -   a sample analyzer configured to produce a signal for            chromosome 15q26 copy number from a cancer cell sample of a            cancer patient; and        -   a computer sub-system programmed to calculate, based on the            mRNA whether the signal is greater or not than a reference            value.    -   100. The system of paragraph 99, wherein said computer        sub-system is programmed to compare the mRNA to determine        -   a likelihood of responsiveness of said cancer cell to            platinum-comprising cancer therapy and/or or a            anthracycline-comprising cancer therapy based on an            algorithm that classifies the patient as likely to respond            to a platinum-comprising therapy if there is a chromosome            15q26 copy number gain and as unlikely to respond to the            platinum-comprising therapy if there is not a chromosome            15q26 copy number gain or if there is a chromosome 15q26            copy number loss.    -   101. The system of paragraph 99-100, wherein the reference value        is chromosome 15 centromere copy number in the sample.    -   102. A computer program product embodied in a computer readable        medium that, when executing on a computer, performs steps        comprising:        -   detecting chromosome 15q26 copy number in sample comprising            a cancer cell from a cancer patient; and        -   comparing the chromosome 15q26 copy number to a reference            value.    -   103. The computer program of paragraph 102, wherein the        reference value is chromosome 15 centromere copy number in the        sample.    -   104. A diagnostic kit for detecting a likelihood of a cancer        patient to respond to platinum- or anthracycline-comprising        cancer therapy, comprising:        -   no more than 10 probes comprising a combination of            detectably labeled probes or primers for chromosome 15q26,            and optionally for chromosome 15 centromere; and        -   the computer program product of Paragraph 102.    -   105. Use of a plurality of oligonucleotides comprising no more        than 10 oligonucleotides capable of hybridizing to chromosome        15q26, and optionally for chromosome 15 centromere, in a        diagnostic kit for determining an increased likelihood that a        cancer patient will respond to cancer treatment regimen        comprising a platinum and/or anthracycline.    -   106. The use, method or assay of paragraphs 65-105, wherein said        anthracycline is epirubincin or doxorubicin.    -   107. The use, method or assay paragraphs 65-105, wherein said        platinum comprising cancer therapy comprises cisplatinum or        cis-diamminedichloroplatinum, phenanthriplatin, carboplatin,        oxaliplatin, or a platinum complex that is activated by        ultraviolet A light.

The following examples are provided to better illustrate the claimedinvention and are not to be interpreted as limiting the scope of theinvention. To the extent that specific materials are mentioned, it ismerely for purposes of illustration and is not intended to limit theinvention. One skilled in the art may develop equivalent means orreactants without the exercise of inventive capacity and withoutdeparting from the scope of the invention.

Example 1

Two clinical trials with cisplatin given to women with triple negativebreast cancer were evaluated.

Cisplatin-1 (DFHCC 04-183; Silver et al., JCO 2010): 28 TNBC patientsreceived neoadjuvant cisplatin as single agent. 10 (36%) achieved atleast 90% reduction in tumor size. Good quality RNA and DNA wereacquired from 21 tumors. Copy number and gene expression were assayedusing AFFYMETRIX arrays.

Cisplatin-2 (DFHCC 06-202; Ryan et al., JCO 2009): 51 TNBC patientsreceived neoadjuvant cisplatin in combination with the angiogenesisinhibitor bevacizumab.

-   -   44 patients completed therapy. 17 (39%) achieved at least 90%        reduction in tumor size. Frozen DNA samples were acquired from        24 tumors, mRNA from 21. Copy number and gene expression assayed        using AFFYMETRIX arrays.

Example 2

In order to find regions or genes where gain or loss were significantlyassociated with sensitivity of resistance cisplatin, ˜40,000 SNP probeswere used in Cisplatin-1 trial and ˜330,000 SNP probes were used inCisplatin-2 trial to determine sensitivity and resistance. GISTICidentified chromosomal regions that were significantly enriched ineither group. Gene copy number comparison showed that genessignificantly gained or lost between sensitive and resistant cases, inboth cohorts. Comparison to gene expression showed overlap with genesshowing differential expression between sensitive and resistant cancers.See e.g., FIGS. 1-3.

Example 3

In a comparison to gene expression data, the inventors found genes thatshow both significant gain and higher expression in sensitive sample. InCisplatin-1 trial, there were 21 cases; Cisplatin-2 trial, there were 21cases. In an ovarian cancer trial (OV-01 trial; Ahmed et al., CancerCell 2007), the two arm carboplatinum had 15 cases and paclitaxel had 19cases. A leave-one-out analysis of the gene expression data wasperformed from both platinum breast cancer trials and the carboplatinumarm of OVO1. See e.g., FIGS. 4-5.

Example 4

In evaluating Hess et al., JCO 2006; Popovici et al., Breast Cancer Res2010; and Andre et al., Clin Cancer Res 2009, expression of BLM or FANCIis not found to be associated with response to multi-agent chemotherapyregimens in TNBC. See e.g., FIG. 6.

Example 5

In evaluating Desmedt et al., JCO 2011, BLM is associated with responseto single agent epirubicin. See e.g., FIG. 7.

Example 6 Chromosome 15q26 Copy Number and Overexpression of BLM andFANCI Predict for Cisplatin Sensitivity

To elucidate if particular genomic aberrations may affect cancer cellssensitivity to cisplatin, we compared the tumor DNA copy number profilesin sensitive versus resistant TN breast tumors in the two separatecisplatin clinical trials. We identified several sites of DNA copynumber change in each trial, but only a short 15 megabase (MB) region onchromosome 15q26 was significantly different between responders andnonresponders in both trials. In addition to SNP profiles, we haveanalyzed the pretreatment tumor samples for both Cisplatin1 andCisplatin2 for mRNA expression profiles on Affymetrix microarrays. Inaddition, gene expression array data was publically available from thecarboplatin arm of a previously published two-arm trial of carboplatinand paclitaxel in serous ovarian cancer[31]. To determine if anyspecific genes were consistently differentially expressed in platinumsensitive compared to resistant tumors, we performed a leave-one-outanalysis in each trial, where we in each round compared the sensitive tothe resistant tumors, and scored how many genes showed a significantassociation. We found that only 3 genes were consistently significantlydifferent in all three platinum-based trials: MCM2, BLM, and FANCI.Interestingly, FANCI and BLM are both located on 15q26.1 and theproteins have been shown to localize to sites of DNA damage. This showsthat using two different methods measuring two different biomolecules,high levels of BLM and FANCI DNA and mRNA is associated with greatersensitivity to platinum-based chemotherapy.

To investigate if higher expression of BLM and FANCI were specificallyassociated with platinum chemotherapy response, we analyzed the geneexpression in the paclitaxel arm of the ovarian trial[31], and acrossthe TN breast cancer subset of three neoadjuvant cohorts that receivedtaxane-containing combination chemotherapy[32-34].

In the ovarian paclitaxel trial and in the TN subset of thetaxane-containing multidrug trials there was no association betweeneither BLM or FANCI and therapy response. These data suggests that highexpression of BLM and FANCI are possibly specifically associated withsensitivity to DNA damaging agents like the platinum salts, but not withresponse to chemotherapeutics that alter microtubules such as taxanes.

We combined the mRNA results into a predictive gene signature: (BRCA1mRNA)/(average of FANCI and BLM mRNA). ROC analysis demonstrates thatthis 3gene mRNA signature is significantly associated with cisplatinresponse in both TN cisplatin trials (FIG. 10A). A prediction modelcombining NtAI and the 3 gene signature improved the prediction ofcisplatin sensitivity (FIG. 10B). Based on the combined model, 25% ofcases are “biomarker positive” with predictive accuracy of 0.86, apositive predictive value of 0.89, a negative predictive value of 0.85,sensitivity of 0.67, and specificity of 0.96 with a p-value of 0.00016.

Example 7 Optimization of BRCA1-BLM-FANCI mRNA Measurement

Several different RT-PCR primer pair assays will be designed to measuremRNA expression for each of the three genes. Data from the Cisplatin2trial comparing the BRCA1, BLM, and FANCI mRNA levels on microarray tomRNA levels as measured by quantitative real-time PCR and found goodcorrelation. The 3-gene predictive model of BRCA1/(avg of BLM+FANCI)using the RT-PCR measurements performed very well for prediction ofcisplatin response (FIG. 11).

Example 8

Platinum salts are effective treatment and standard therapy for a numberof cancer types including serous ovarian carcinoma, high gradeurothelial carcinoma, pancreatic adenocarcinoma, glioblastomamultiforme, and lung squamous cell carcinoma. Breast adenocarcinomasarising in women carrying BRCA1 or BRCA2 mutations are also sensitive tocisplatin chemotherapy (Byrski, 2008). BRCA1 is a tumor suppressor thatplays important roles in several aspects of maintenance of genomeintegrity. Complete absence of functional BRCA1, as occurs in tumors ofBRCA1 mutation carriers with loss of the wild-type allele, leads todefective error-free homologous recombination-type double strand breakrepair. These BRCA1−/− tumors are sensitive to inhibitors of PARP1 (ref)whereas, so far, few or no sporadic BRCA wild-type breast cancers haveresponded to these agents. Recent studies have shown that in addition todouble strand break repair, BRCA1 also plays an important role inresponse to replication stress and repair of stalled or collapsedreplication forks (Pathania, 2011). Preliminary evidence suggests thereplication repair functions of BRCA1 may be haploinsufficient in BRCA1heterozygous cells (Pathania, unpublished data). The platinum saltsgenerate interstrand and intrastrand crosslinks that distort DNA andlead to stalled replication forks. If these stalled forks collapse,double strand breaks will results. It is possible that severalBRCA1-dependent pathways are involved in platinum-induced DNA damageresponse including damage recognition and lesion excision, suppressionof translesion synthesis, checkpoint activation, and repair of DS breaksafter fork collapse.

The activity of cisplatin has recently been extended to estrogen,progesterone, and HER2 receptor negative sporadic breast cancers(triple-negative breast cancers, TNBC)(Silver, 2010; Birkbak, 2012;Ryan, 2009). When carboplatin was added to anthracycline and taxanechemotherapy for treatment of TNBC, the response rate was higher butresulted in notably greater toxicity. Predictors of tumor response toplatinum salts are needed to determine which patients may derive thegreatest benefit from the addition of platinum. Previous molecularstudies have shown the platinum-sensitive TNBC and serous ovariancancers carry high levels of genomic rearrangements and chromosomalallelic imbalance, suggesting these cancers may share similar defects inDNA repair, which may make them particularly sensitive to platinumchemotherapy (Birkbak, 2012). Many of the platinum-sensitive sporadicTNBCs have promoter methylation and reduction in the expression of BRCA1(Birkbak, 2012; Silver, 2010). These result suggests that platinumsensitivity may be related to a functional defect that occurs when thereis insufficient BRCA1 levels, raising the possibility that defects in ahaploinsufficient function of BRCA1, such as replication-dependentstalled fork repair, may be indicative of sensitivity to interstrandcross-linkers such as the platinum salts.

To further explore and define other specific molecular alterations thatmight be associated with cisplatin sensitivity, we took and integratedgenomic approach combining differential analysis of gene expression andDNA copy number in cisplatin sensitive compared to cisplatin resistanttriple negative breast cancers. We identify two genes, the Bloomhelicase (BLM) and Fanconi anemia complementation group I (FANCI), thathave both increased DNA copy number at chr 15q26 and concordant mRNAoverexpression in the TNBC with increased sensitivity to cisplatintherapy. In vitro modulation of BLM and FANCI expression suggest thesetwo genes play a functional role and promote DNA damage and sensitivityto platinum salts, but have no effect on taxane sensitivity.

Identification of genes critical for tumor response to specificchemotherapy drugs is a challenge, but important for tailoring therapyand avoiding unnecessary toxicity in patients. Integrated genomicapproaches that combine DNA copy number analysis with gene expressionprofile analysis has successfully indicated genomic alterationsassociated with chemotherapy resistance and tumor response (Li, 2010).We have previously published the results of two trials of cisplatinchemotherapy in TNBC in which presurgical treatment with cisplatinresulted in greater than 90% reduction in tumor volume in 36% and 39% ofpatients respectively (Silver, 2010; Ryan, 2009). Molecular inversionprobe SNP copy number profiles of pretreatment tumors from bothcisplatin TNBC trials were reported previously (Birkbak, 2012). Geneexpression profiles from the pretreatment tumor samples from the firstcisplatin TNBC trial were also reported previously (Silver, 2010). Forthis study, we generated gene expression profiles from the pretreatmenttumor biopsies from the second cisplatin TNBC trial.

To determine genes whose expression is significantly and robustlyassociated with response to cisplatin, we performed a leave-one-outdifferential gene expression analysis in each trial, comparing the geneexpression of tumors resistant to cisplatin to tumors that weresensitive to cisplatin. For each leave-one-out round, one sample wasremoved and all genes significantly associated with response weredetermined. The direction of association for each gene (higher insensitive vs. lower in sensitive) was also noted. Permutation testing ofthis gene expression comparison exercise indicated that a gene must bepresent in 85% or more rounds to be significant. This analysisidentified only 12 genes whose expression was significantly associatedwith platinum response, in the same direction, in at least 85% of allrounds in both cisplatin TNBC cohorts.

We performed next a similar leave one out comparison analysis of the DNAcopy numbers of cisplatin sensitive vs. cisplatin resistant TNBC tumorsin the two trials. Permutation testing of the DNA copy number LOOanalysis indicated that a gene must be present in 50% or more LOO roundsto be significant. This analysis identified 234 genes from fourdifferent chromosomes with differential copy number associated withcisplatin response in at least 50% of all rounds in both cisplatin TNBCcohorts.

Only two genes were identified in both the DNA copy number and geneexpression leave-one-out analyses for association with platinumsensitivity, Bloom helicase (BLM) and Fanconi anemia complementationgroup I (FANCI), both located at chromosome 15q26. The DNA copy numberof the 15q26 region containing these two genes was significantly higherin the cisplatin-sensitive tumors in both TNBC cohorts (p=0.00236 andp=0.0107, respectively. Similarly, cisplatin sensitive tumors hadsignificantly higher BLM expression in both TNBC cohorts (cisplatin-1,mean log 2 expression, 8.26 versus 7.54, p=0.00278; cisplatin-2, meanlog 2 expression, 10.67 versus 9.41, p=0.00745; FIG. 1C-D). FANCIexpression was higher in the cisplatin-sensitive TNBCs in both cohorts(cisplatin-1, mean log 2 expression 7.87 versus 6.80, p=0.00356;cisplatin-2, mean log 2 expression 10.74 versus 9.77, p=0.0125).

The gene expression of BLM and FANCI as measured by Affymetrix U133array was validated by RT-PCR in the same samples and the results showedgood correlation (BLM, r=0.866; FANCI, r=0.733). BLM (and FANCI) arereported to have post-translational mechanisms of protein regulation. Todetermine if overexpression of BLM and FANCI mRNA also results inincreased expression of the protein, we measured BLM (and FANCI) proteinby western blot analysis in protein extracts from a series of frozenbreast tumor samples for which mRNA gene array expression levels wereknown (Lu, 2008). BLM normalized to actin (and FANCI) showed goodcorrelation between mRNA expression levels and protein expression levels(r=0.70).

BRCA1 as measured by RT-PCR was identified in our previous studies assignificantly associated with cisplatin resistance (Birkbak, 2012;Silver, 2010). In contrast to BLM and FANCI, BRCA1 expression asmeasured by microarray was poorly correlated with expression as measuredby RT-PCR (r=xxx); the microarray BRCA1 probe performance was especiallypoor in the data from first cisplatin TNBC cohort. Therefore, we usedthe RT-PCR expression data to test the association of the ratio ofBRCA1/average (BLM+FANCI) expression and cisplatin response. The ratiowas significantly higher in the cisplatin sensitive tumors in bothcohorts (cisplatin-1, median x vs y, p=0.023; cisplatin-2, median 7.69vs 4.07, p=0.0016).

To validate these specific gene associations with platinum response, wetested a publically available gene expression data set from a serousovarian cancer trial of either carboplatin monotherapy or paclitaxelmonotherapy and sought associations with response to the therapyreceived. The average expression of BLM and FANCI was significantlyhigher in the carboplatin-sensitive ovarian cancers (median 5.46 versus4.50, p=0.026). The ratio of BLM+FANCI/BRCA1 was also significantlyhigher in carboplatin sensitive ovarian cancers (median 1.29 vs 0.42,p=0.026). Interestingly, the association of BLM and FANCI withpaclitaxel response was not significant and the trend was in theopposite direction (median 5.17 versus 4.79, p=0.27).

We also showed protein abundance of BRCA1, BLM, FANCI, and Cyclin A wasmeasured by Western blot analysis in protein extracts from a panel ofbreast cancer cell lines. The bands were quantitated by densitometry anddisplayed in bar plots. We showed the quantitation of BLM to Actin andBRCA1 to BLM ratio. Three cell lines (BT549, HCC1143, and HCC38) arenormal genotype for BRCA1 and have high BLMIActin and low ratio ofBRCA1/BLM. Two cell lines (MDA231 and MDA453) are also normal genotypefor BRCA1 but have relatively higher expression of BRCA1/BLM and lowerBLM/actin. HCC1937 and MDA436 have homozygous mutation in BRCA1 andundetectable BRCA1/BLM, and higher expression of BLM/Actin.

A panel of cell lines was evaluated for sensitivity to varioustreatments as indicated by colony formation assay and calculation ofIC50 values. We showed a pattern of sensitivity to cisplatin, UVradiation treatment, and Parp inhibitor Olaparib across the panel ofcell lines is associated with the pattern of relative expression ofBRCA1/BLM and BLM/Actin. The two BRCA1 mutated cell lines and the threecell lines with low BRCA1/BLM and high BLM/actin have greatersensitivity to DNA strand cross-linker cisplatin, PARP inhibitorOlaparib, and UV irradiation. The two cell lines with low BLM and highBRCA1/BLM (MDA231, MDA453) are relatively resistant to these treatments.In contrast, there is no apparent association between BLM and BRCA1expression with the pattern of sensitivity to the microtubule stabilizerPaclitaxel.

We also treated U2OS cells treated shRNA to BRCA1. After 1 week, theexpression of BRCA1 and BLM were measured by Western blot analysis.Cells treated with the BRCA1 specific shRNA showed increased expressionof BLM compared to control cells treated with shRNA to luciferase.

We further treated BT549 breast cancer cells, with inherent high levelsof BLM and FANCI were treated with gene-specific siRNAs to BLM or FANCIor with a scramble control. Gene specific siRNA treatment resulted inreduced mRNA expression as determined by RT-PCR. Sensitivity tocisplatin and to paclitaxel was determined by colony formation assay tocalculate the IC50. siRNA knockdown of either BLM or FANCI resulted inincreased IC50 (greater resistance) to cisplatin treatment but nosignificant effect on sensitivity to paclitaxel.

MDA231 cells have low levels of BLM and relative resistance tocisplatin. These cells were used in experiments to assess the effect ofincreasing the expression of BLM. A lentivirus expression vector forHA-tagged BLM cDNA or a control vector was transfected into MDA231cells. BLM expression was assessed by Western blot analysis forendogenous BLM or for the HA-tag in cells treated with control vector,BLM cDNA, BLM cDNA and a small molecule inhibitor of BLM helicase(BLMi), or BLM cDNA and BLM siRNA. We showed that siRNA for BLM reducedthe expression of endogeneous and HA-tagged BLM whereas the smallmolecule inhibitor (BLMi) had no effect on protein expression of BLM.

IC50 for cisplatin was determined by colony formation assay in MDA231breast cancer cells treated with control vector, BLM cDNA vector, BLMcDNA plus the BLM small molecule inhibitor, and BLM cDNA plus BLM siRNA.Overexpression of BLM resulted in decrease in the IC50 (greatersensitivity) to cisplatin. Consistent with the other findings, thiseffect was reversed by treatment with the BLM helicase inhibitor and bysiRNA knockdown of BLM.

We also performed an immunofluorescence assay for markers of DNA damage(H2Ax-p and 53BP1-p) in MDA231 cells treated with control vector, BLMcDNA, BLM cDNA+BLM inhibitor, or BLM cDNA+BLM siRNA. Overexpression ofBLM results in increased H2AX and 53BP1 foci in the absence of anycisplatin treatment indicating spontaneous DNA damage. This effect iseven greater in cells treated with cisplatin after 4 hours. Thequantitation of foci is shown in the lower bar graphs. The addition of asmall molecule BLM helicase inhibitor (Bi) or siRNA to BLM (si) blocksthe effect of BLM overexpression on DNA damage foci.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein arehereby incorporated by reference in their entirety as if each individualpublication, patent or patent application was specifically andindividually indicated to be incorporated by reference. In case ofconflict, the present application, including any definitions herein,will control.

Also incorporated by reference in their entirety are any polynucleotideand polypeptide sequences which reference an accession numbercorrelating to an entry in a public database, such as those maintainedby The Institute for Genomic Research (TIGR) on the world wide weband/or the National Center for Biotechnology Information (NCBI) on theworld wide web.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

Various embodiments of the invention are described above in the DetailedDescription. While these descriptions directly describe the aboveembodiments, it is understood that those skilled in the art may conceivemodifications and/or variations to the specific embodiments shown anddescribed herein. Any such modifications or variations that fall withinthe purview of this description are intended to be included therein aswell. Unless specifically noted, it is the intention of the inventorsthat the words and phrases in the specification and claims be given theordinary and accustomed meanings to those of ordinary skill in theapplicable art(s).

The foregoing description of various embodiments of the invention knownto the applicant at this time of filing the application has beenpresented and is intended for the purposes of illustration anddescription. The present description is not intended to be exhaustivenor limit the invention to the precise form disclosed and manymodifications and variations are possible in the light of the aboveteachings. The embodiments described serve to explain the principles ofthe invention and its practical application and to enable others skilledin the art to utilize the invention in various embodiments and withvarious modifications as are suited to the particular use contemplated.Therefore, it is intended that the invention not be limited to theparticular embodiments disclosed for carrying out the invention.

While particular embodiments of the present invention have been shownand described, it will be obvious to those skilled in the art that,based upon the teachings herein, changes and modifications may be madewithout departing from this invention and its broader aspects and,therefore, the appended claims are to encompass within their scope allsuch changes and modifications as are within the true spirit and scopeof this invention. It will be understood by those within the art that,in general, terms used herein are generally intended as “open” terms(e.g., the term “including” should be interpreted as “including but notlimited to,” the term “having” should be interpreted as “having atleast,” the term “includes” should be interpreted as “includes but isnot limited to,” etc.).

What is claimed is:
 1. A method for treating cancer in a human subjectin need thereof comprising the step of administering ananthracycline-comprising cancer therapy to the human subject when thecancer in the human subject has been determined to have increasedexpression of BLM and FANCI compared to a reference value.
 2. A methodof treating cancer in a human subject, comprising administering ananthracycline-comprising cancer therapy to a human subject when a cancercell taken from the human subject has been or is determined to carry achromosome 15q26 copy number gain compared to a reference value.
 3. Themethod of claim 2, further comprising the steps of detecting achromosome 15q26 copy number in a sample comprising a cancer cell takenfrom the subject; comparing the chromosome 15q26 copy number to areference value.
 4. The method of claim 2, wherein the cancer isselected from breast cancer, ovarian cancer and lung cancer.
 5. Themethod of claim 2, wherein the subject's cancer is known to not expressa detectable quantity of ER, PgR, and HER2 receptor.